Another poster had mentioned Prussia and this is a good example of the importance of titles with the interrelations of the rulers with each other. The house of Hohenzollern were prince-electors of Brandenburg (within the Holy Roman Empire) but from 1618 also ruled the Duchy of Prussia (which was outside the Holy Roman Empire, and for a while under the Kingdom of Poland, making the head of Hohenzollern the Prince-Elector of Brandenburg under the Holy Roman Emperor, and Duke of Prussia under the King of Poland). In 1700, after Frederick III (Elector and Duke) supported Leopold I (Holy Roman Emperor) in the Spanish War of Succession, as a reward Leopold I agreed to recognise Frederick III as King in Prussia (crucially not King of Prussia), because in theory Frederick was not a king within the Holy Roman Empire (only within his Prussian territory beyond the Empire). There were also reasons such as the historic Kingdom of Prussia having larger territory than the current Duchy of Prussia, and so assuming the title King of Prussia could have been interpreted as Frederick having designs on territory which was now part of other kingdoms, such as Poland. In wasn't until 1772 that the title of King of Prussia was claimed, after Frederick II (grand-son of Frederick III, who became confusingly Frederick I as King in Prussia) had won a lot of power and land.

Lithuania is similarly if not more complex. It was briefly a kingdom, after Mindaugas was crowned King 1253. Prior to that he had been a Grand Duke, but after agreeing to convert to Christianity, the Pope agreed to recognise him as King of the Kingdom of Lithuania (don't forget it was also the Pope who crowned Charlemagne the first Holey Roman Emperor). The situation in Lithuania at this time was complex, as it was still largely pagan, and there was a lot of fighting and struggles for power, in which the Teutonic Order (Livonian Order) were involved in. It seems Midaugas was only a Christian for strategic purposes, and may have reverted back to paganism. Either way, most of Lithuania and its nobility remained pagan, and Midaugas was assassinated, and Lithuania fell into internal strife and was ruled by pagans who were recognised only as Grand Dukes, not Kings (at least in the eyes of the rulers of Christian Europe).

Lithuania was Christianised in 1387, under the reign of Jogaila . I can't find anything that comes right out and says it, but in my opinion, crucially for the status of Lithuania, while Jogaila was already Grand Duke of Lithuania as a pagan, he became Christian as part of his marriage to Jagwiga, Queen of Poland (which was already a well established Catholic Kingdom), and so became Christian King of Poland and Grand Duke of Lithuania. This started off the Poland-Lithuania Union, with Poland remaining a Kingdom and Lithuania a Grand Duchy, even though Lithuania was now Christian. When Jogaila became King of Poland he left a regent to rule Lithuania as Grand Duke, and there was a lot of power struggling and fighting between families to be the Grand Dukes. The King of Poland and Grand Duke of Lithuania didn't resume being the same person till Casimir IV became King of Poland in 1447. This meant that Lithuania was sort of the junior partner in this relationship going forward (a little like the ruler of Austro-Hungary being Emperor of Austria and King of Hungary).

Therefore, in summary and with my interpretation: Lithuania's pagan status meant in was not recognised by Christian Europe as a true Kingdom, and Lithuania's lateness in joining Christian Europe meant that by the time in joined their ranks there were already many established Christian kingdoms around, who were unlikely to desire a new competitor for prestige. Coupling this with its union to the already well established kingdom of Poland meant that the Grand Dukedom remained a lesser title which the king of Poland possessed.

I may be able to help you because my bachelor-thesis on the Teutonic Order covers some parts of your question. I want to add that my native language is not english.

First of all, i would call Lithuania only "empire" in a wider sense of the term meaning a big realm that's controlled by one head of state. Technically there was no "emperor" of Lithuania. But let's start at the beginning.

Around the year 1293 Vytenis became the leader of Lithuania, uniting the nobles of the country under his banner after years of infighting. He started expanding his realm to the south and east. After his death, his brother Gediminas continued this. They also fought against the Teutonic Order that was situated around todays Kalinigrad. The Order was also fighting against the kingdom of Poland because of some border issues; the order had annihilated some lands of Poland. Both realms were interested in a pact against the mighty crusaders.

In 1368 the king of Poland was dead, and his queen married the ruler of Lithuania, Jagiello. He got baptized and named himself Wladislaw. His brother became "grand-duke" (i can't translate the title, it's Großfürst in german) of Lithuania and henceforth Poland and Lithuania were one big kingdom. At the beginning of the 15th century the kingdom took down the Teutonic Order and claimed their lands, creating a big realm in the east of Europe.

Still, the king of Poland-Lithuania was only a king, never an "emperor" (or Kaiser as it's called in german). I haven't covered the history of Poland-Lithuania after 1450 so i can't tell you what happened later and how this union ended, but i'm quite sure that the pope never made the king of Poland-Lithuania an emperor because the Habsburgers had this title at this time (Friedrich II., Maximilian I., Karl V. and so on).