I think the question here is not whether there really were atrocities under Stalin but to what extent Stalin the person was responsible. If we take the paragraph you cited as an example of a set of common allegations, it would be wise to address them individually.

Stalin built up a cult of personality around himself

No one would claim that there was not a cult of the individual surrounding Stalin, but the story is likely more complicated than this. Stalin himself likely did not "invent" the leadership cult, nor is the word "invent" really appropriate to the gradual adoption of a number of practices by the group of Stalinist leaders. The leader cult did not begin until as early as 1930, but really kicked off in 1933 when Stalin, who in the 1920s was a rather mysterious and anonymous bureaucratic figure in the public eye, began to be called 'beloved Stalin' in official discourse. But the issue to keep in mind is that the public veneration of leaders did not end with Stalin. Other members of the leadership like Kaganovich, Voroshilov, Ordzhonikidze, Kalinin, Molotov, and others were also praised effusively in public discourse. The cult extended to the public veneration of workers who served as examples for the nation and for socialism. Of course, these were like saints and heroic figures orbiting the monotheism of Stalin.

that Stalin suppressed democracy and eliminated anyone who disagreed with him

It appears actually that Stalin tried to use democracy to eliminate those who obstructed him, at least in the 1930s. It is a somewhat inappropriate notion to discuss treatment of those who 'disagree' in a political sphere like the USSR where the dominant political party did not think of politics as a debate, but as a struggle. The bigger problem for Stalin and the other central leaders was the lack (often real and not merely perceived) of control over peripheral political matters. The targets of their ire were often the party secretaries who carved out political machines for themselves away from Moscow. In 1936, Moscow appears to have invested considerable political capital in the fulfillment of promises of democracy as part of the new Constitution. Critics have frequently claimed that Stalin had no interest in democracy and this was clearly a ruse, but that seems a bit oversimplified given recent archival material. Internally Stalin and his cohorts appear to have been very earnest about their desire to expand democratic rights. J. Arch Getty has written on this, concluding that the reasoning was likely twofold: First, as a gesture of goodwill (and propaganda) to Britain and France in a climate of escalating tensions with Germany, and second, as a means of using mass political mobilization to discipline the regional party secretaries. In this light, the terror of the next two years makes more sense, given that its targets were largely those same secretaries rather than ordinary people.

It is worth noting here that Stalin in the 1920s opposed intra-party democracy in a time of in-fighting, which gained him great support from the party secretaries, but came to endorse it later in the mid-1930s for the above reasons. This would place Stalin firmly in the camp of 'politician' whose vacillations reflect changing political circumstances and pragmatic interests. I am less fond of explanations that attribute such changes in attitude to Stalin's far-reaching and diabolical plans for personal dictatorship. Politicians change attitudes on practical matters of policy frequently, often within a window of time far shorter than this period of 10 or so years.

that the bureaucracy which emerged in the USSR was largely Stalin’s doing

That is a burdensome allegation to levy on a single person. It seems to me that this would rest on the notion, often extended but rarely studied in depth, that Stalin weaseled his way into power by using his power of appointments as General Secretary to eliminate enemies and promote allies. In so doing, perhaps, Stalin eliminated all 'true revolutionaries' and replaced them with stodgy conservative bureaucrats. James Harris in "Stalin as General Secretary: the Appointments Process and the Nature of Stalin's Power" addresses this very question and concludes that in the wake of Lenin's death, the succession struggle took over all levels of Soviet politics. He concludes that his position as Secretary was critical in his rise to power, as he was able to quiet the political struggles which earned him great support from the various party secretaries, but that there is scant evidence that he used his position as General Secretary to further a personalistic dictatorship.

The bureaucracy was not a creation of Stalin, but was a factor in his rise to prominence. Trotsky claimed just the same, often downplaying Stalin the man to an incredible and unwise extent. Furthermore, I think the notion that Stalin ended the revolution to be rather simplistic. Trotsky called this the Soviet 'Thermidor,' which is a comparison more apt than he knew. For Trotsky, Thermidor was a conservative reaction against the radicalism of the Jacobins. It was, in a sense, a counter revolutionary force designed to fix certain changes and eliminate more radical ones. Yet more recent scholarship of the French Rev seems to show that the Thermidoreans were revolutionaries through and through, but just not Jacobins. They were still rather radical, but in a different sort of way. Similarly, the Stalinist regime did not pull its proverbial foot off the gas after 1924. They were the ones who abandoned the NEP to pursue an economic plan similar to that which Trotsky's cohorts in the Left-opposition had supported. In so doing the USSR became a radical beacon of anti-capitalism to a world facing a disintegrating liberal order and collapsing global economy. It seems to me this particular criticism - which is often levied by the left rather than the right - does not adequately address the question of whether or to what extent the various political problems the USSR faced in the 1930s were related to the process of industrialization itself, and the social upheaval associated with it. European Marxists had traditionally been hostile to peasants in general, Trotsky among them. It is far from clear in my view that Stalin the person was the decisive factor in the escalation of struggle and repression in the countryside from 1929-31 (and beyond), or that the resulting collisions and disquiet was within the control of a single personality. Perhaps I merely think individual humans are far less powerful than we or even they tend to believe.

The allegations of terror have teeth, but the focus on Stalin often obscures the various other factors involved. For example, in the collectivization period there was a great amount of repression directly authorized and encouraged by the central authorities (Stalin most prominent among them, but not overwhelmingly so at this point in 1929ish). But a good deal of the repression was the unleashing of age old social tensions in the countryside, often with a village to village flavor. The terror of 1936-38 seems somewhat similar in the sense that the center certainly uncorked the bottle, but what came out was beyond their control or understanding. I have written some long posts on the issue of the terror in more detail which you can find here, here, and here.

I would recommend Anne Appelbaums 'Gulag' as an excellent read on the subject of Stalins treatment of prisoners and dissidents. It shows how Stalins paranoia of not only people around him, but the Soviet people also led to many deaths and imprisonments

Short answer: yes, even more than you ask about. Stalin's crimes are comparable to anything Hitler or Mao did. Stalin used torture and murder on a massive, massive scale. Literally millions of Soviet citizens were tortured, killed, or exiled by Stalin's purges. And that's not even getting into the famines in the Ukraine in the 1930s, which were deliberately induced and led to millions upon millions of Ukrainian deaths.

Bloodlands by Tim Snyder is an excellent (and very readable) resource on all the atrocities that happened under Stalin.

I'm a big fan of socialism but when it comes to history, some people, so caught up in ideology have a tendency to be really revisionist. Stalin really was responsible for the ascendency of bureaucracy in the Soviet Union, he had orchestrated his rise to power over Trotsky through the use of party politics and favors, and that trend was present throughout his rule. While he wasn't corrupt, party became absolutely everything. A common criticism of the USSR is that the ruling class was never abolished, but that aristocrats were replaced by party bureaucrats, and that society's transformation was only superficial because Stalin put a halt to the social revolution. I tend to agree with this, but it really isn't a fact, just an opinion. As far as crimes go, it's just about all true. When Stalin died and Khrushchev came to power he embarked on desalinization and one of the core facets of this was exposing all the crimes of Stalinism. Some apologists insist that Khrushchev was just doing this to build his own image, this may be true, and that everything he said was lies, this isn't true. So it isn't just western historians making up facts to criticize Stalin, much of the atrocities were exposed during the Soviet Era, and many more were exposed in released soviet files when the Soviet Union dissolved. Those files continue to be released and it has become apparent that there is no shortage of atrocities under Stalin.