This is obviously a value question, and no doubt many will condemn Trotsky for his role in the original Revolutionary government under Lenin and as the commander of the Red Army during the brutal civil war - though I believe the context of that civil war demands we judge Trotsky no harsher than we'd judge any other commander or general in a time of desperate and dire warfare (such as Sherman or Grant, etc.)

But as to your question, I also believe it's difficult to even compare Trotsky and Stalin due to the immense crimes against humanity and totalitarian excesses committed under the latter. To prove my point: Trotsky himself offers many critiques of Stalin's turn away from democratic centralism (the Bolshevik practice of debate and democratic decision-making amongst party members which would result in unified and mandatory positions and action). Trotsky himself, a long time Menshevik prior to 1917 (the democratic socialist faction which competed with the Bolsheviks for control of the Soviets), had long been an advocate for more democratic-oriented socialist practice, as opposed even to Lenin. Trotsky helped to author The Declaration of 46 in the wake of Lenin's decline and the rise of the Stalinst right-wing faction, which critiqued the lack of democracy within the party and the rise of bureaucratic authoritarianism resulting from the divorce of party delegates from the masses (during the civil war delegates began to be appointed rather than elected). Trotsky was also highly critical of Stalin's deification of Lenin, revision of history, cult of personality, and of the summary executions and purges undertaken by Stalin against almost all original Bolshevik leaders in the revolution. The Trotskyist critique of Stalin's theory of Socialism in One Country arguably also anticipated and opposed the authoritarian tactics that would come to be adopted by Stalin and other oppressive Marxist-Leninist regimes to come.

Sources: Trotsky's biography of Stalin - this is a great and fascinating first hand look into the devolution of the party into Stalinism over the long term. Obviously, it's biased, as Trotsky is the one who wrote it, but he clearly lays out policy and theoretical differences between Stalin and Lenin/other original party members. It is well sourced as well, and he does a good job establishing an extent of objectivity.

Rabinowitch's The Bolsheviks Come to Power shows the surprisingly lively and open debates occurring in the party up to the Revolution, where challenges to Lenin's positions were the norm - a far cry from the party under Stalin.

Also see his: Politics and Society in Pterograd 1917-1920

And Suny's The Soviet Experiment

Edit: grammar

The comparison with Trotsky is difficult to make as Trotsky never lead the Soviet Union. It is impossible for historians to say what a Trotsky-led Soviet Union would have looked like. What we do know, is that Trotsky was a political thinker who turned out to be a successful military commander, and the person Lenin wanted to lead the Soviet Union. This of course never happened since Stalin was able to maneuver his way into absolute power. Trotsky did defend the terror practiced by the fledgling Bolshevik government during the Russian Civil War and Polish Campaign, but again as he never led the Soviet government, we will never know if he would have a death toll as high as Stalin’s or if the Soviet Union would have turned into the paradise promise by Bolshevik revolutionaries. My personal area of expertise with Russia/Soviet Union is from Stalin onwards, so I will therefore focus on why so many are critical of Stalin. However, when examining Stalin’s actions, one can see why Trotsky, whose political downfall and eventual execution were engineered by Stalin, is viewed in a favorable light.

The negative perception of Stalin stems from the millions of Soviet citizens who died as a result of his policies from 1930 through his death in 1953. During this twenty three year period, around 9 million civilians died as a direct result of Stalinist policy. These deaths came as the result of terror and famine, two of the key elements Stalin used to fast track Soviet industrialization and expansion. Additionally, Stalin’s actions before and during World War II led to the near collapse of the Soviet front in 1941, unnecessary deaths that came as a result of poor military doctrine, and war crimes committed against Soviet soldiers and combatants alike.

Stalin’s Five Year Plans were intended to rapidly industrialize the Soviet Union so that it could exist as the only socialist nation in a capitalist world. The core concept of Leninism was that a socialist revolution in a growing nation, such as Russia, would serve as the spark to the world revolution that would soon engulf the Western industrialized nations. This of course did not take place as democratic governments controlled France, Germany, and the United Kingdom throughout the 1920s. Thus, the Soviet Union adopted the theory of “Socialism in One Country,” the idea that the Soviet Union would need to hold firm against intrinsically hostile capitalist nations. As the Soviet Union attempted to establish itself in the 1920s, Lenin’s government implemented the New Economic Policy (NEP), which contained capitalist elements for farmers and small traders. To Stalin, NEP benefited the farmers, not the state, and he came up with the Five Year Plans as a drastic means to enhance the economic and military standing of the nation. Based on the idea that the capitalist nations would not tolerate the existence of a socialist country indefinitely, Stalin’s Five Year Plans were designed to rapidly industrialize and modernize the Soviet Union so that it could survive in a capitalist world.

Stalin used terror to keep control of a large population while NEP was quickly dismantled and replaced with the Five Year Plans. Historian Lynne Viola argues that “terror (was) in fact, the sin qua non (an essential condition; a thing that is absolutely necessary) of Stalinism. In 1928, the Soviet Union was still a primarily agricultural nation, and the peasant farmers did not want to give up their economic freedom. This presented a challenge to one of the main elements of the First Five Year Plan, the collectivization of farms. Under this system, peasants gave up all rights to property and they would work their former lands as part of a ‘collective’ of farmers. Grain was sent to the cities to feed the growing urban workforce and exported to industrialized nations in exchange for technology and machinery. Collectivization was met with resistance, and terror was one of the methods used to quell the peasant population.

Terror was also used to eliminate enemies of Stalinism, including Trotsky, as well as potential political enemies. Stalin eliminated his former political allies in a series of show trials that resulted in execution. Millions of Soviet citizens faced the same fate or years in the gulag for being an ‘enemy of socialism.’ In the vast majority of cases, the accused individuals had not violated any law or attempted to subvert or overthrow the Soviet government. During the Great Purge, 1936-1938, Soviet officials were given mandatory quotas of arrest numbers for their respective areas. The purge extended to the military in 1937-1938, and left most Soviet officers dead, in gulags, or dismissed from command.

Finally, terror was used to wrest control of Estonia, Latvia, Lithuania, and Poland in 1939. In each of these nations, any person that could have been a potential threat to the Soviet takeover was arrested, and sent to a gulag or executed. The most famous example of this is the Katyn Massacre, where over 20,000 Polish soldiers were murder by the Soviet Union.

In addition to the arrests made by Stalin’s government, over 3 million, mostly Ukrainian, Soviet citizens died as the result of famine. As previously mentioned, one of the main economic goals of Stalinism in the 1930s was the collectivization of peasant farms in order to amass grain to feed workers in the city and trade on the export market. Collective farms were given production quotas, and everyone farmers to the political officials responsible for the new system of farm faced dire consequences for missing theses targets set by Moscow. In the first year of collective farming, the inclusion of seed grain was required in order to meet the quotas. Seed grain is normally set aside to be used for planting the following year, meaning that collective farms were losing their future ability to grow wheat in order to meet the first quota. As starvation became rampant in Ukraine, the Soviet government insisted on higher quotas and hauled away grain despite the mass starvation.

Finally, historians are very critical of some of Stalin’s actions during the Second World War. To start with, Stalin had received thousands of warnings from a wide variety of intelligence sources that Hitler was going to break the Molotov-Ribbentrop Pact and attack the Soviet Union. Stalin chose to ignore these warnings and did not bolster the Soviet’s defense in the western part of the nation, nor did he initially allow the Soviet military to fight back against the Nazi invasion. Additionally, Stalin’s earlier purge of the military severely weakened the fighting capabilities of the Red Army and Soviet Air Force. Order No. 270 ensured that Soviet soldiers who surrendered to the Germans were regarded as traitors and their families faced government retribution, usually in the form of losing access to government supplied food and goods. Stalin even refused a prisoner exchange for his son and expressed joy at his son’s suicide in a Nazi POW camp. The infamous Order No. 227 legalized the execution of Soviet soldiers who retreated and prevented local commanders from authorizing withdrawals, no matter the circumstance. Stalin also insisted on disastrous counter offensives, including those after the Battles of Moscow and Stalingrad. Many German POWs were sent to the Gulags, and in the case of those captured at Stalingrad, some were not released until after Stalin’s death in 1953. Finally, Stalin’s government allowed the rape and pillage of Germany as the Red Army approached Berlin.

What, if any, of Stalin’s actions were justified and/or the result or circumstance outside of his control is the subject for another conversation. For the sake of this answer, I have attempted to lay out why many historians view Stalin in such a negative light.

***All of my casualty numbers come from Timothy Snyder. His figures are lower than some other authors, such as Robert Conquest. Snyder’s figures come from a level of access to Soviet records that earlier authors did not have.

Sources:

Bloodlands: Europe between Hitler and Stalin, by Timothy Snyder

Russia’s War: A History of the Soviet War Effort, 1941-1945, by Richard Overy

“Stalin’s Empire: The Gulag and Police Colonization in the Soviet Union in the 1930s,” by Lynne Viola in Stalin and Europe: Intimidation and Domination, 1928-1953, edited by Timothy Snyder and Ray Brandon

“Stalin, Espionage, and Counter Espionage,” by Hiroaki Kuromiya and Andrezj Peplonski in Stalin and Europe: Intimidation and Domination, 1928-1953, edited by Timothy Snyder and Ray Brandon

Hope it’s okay to add a question but any historians here know about Trotsky involvement in the Kronstadt rebellion? As I’ve seen this used before as an example of a negative side to him which might add to OPs question as a counter but I don’t know much myself and always been curious