Vladimir Putin in his recent speech stated that it was Nikita Khrushchev who basically gave Crimea to the Ukrainian SSR taking it from the RSFSR in 1954, despite the fact that 'Crimea has always been an inseparable part of Russia'. This brings an interesting question: how come the same principle doesn't apply to Königsberg, or, as russians call it - Kaliningrad, which, if truth be told, is more german than Crimea is russian? Didn't this town belong to Germany up until 1946, when the soviets invaded it?
How legitimate would Germany's claims for Königsberg be compared to Crimean situation?
The two situations aren't really the same. The transfer of Crimea was internal to USSR. At that point, no one even imagined that Ukraine would one day be an independent country. Thus, Ukraine getting Crimea was little more than an administrative reshuffling.
Kaliningrad was taken by the USSR as a result of of WWII. It was actually Germany that invaded the USSR, not the other way around. Thus Kaliningrad served as a compensation to the Soviet Union for the damage and the losses it suffered as a result of the Nazi invasion. There were strategic reasons as well - East Prussia served as a staging are for the German invasion. In any case, the annexation of Kaliningrad was determined and agreed to by the international treaties following WWII. In fact, Germany itself signed a treaty in 1990 agreeing to the territorial changes that happened in the aftermath of WWII. Thus, Germany doesn't have any claim to East Prussia, at least not anymore than say Mexico has claim to Texas and the rest of Southwestern US.
Kaliningrad, which, if truth be told, is more german than Crimea is russian?
Modern Kaliningrad Oblast is, according to the 2010 census, 86.4% ethnic Russian and 0.8% ethnic German - as in many parts of Europe such as the Czech Sudetenland and western Poland, the German populations were distinctly Persona Non Grata in 1945 and were "encouraged" to resettle in Germany. There's actually a pretty good Wikipedia Article on the subject with lots of references to follow up on if you're interested.
By contrast, Crimea is (according to the 2001 census), 60% Russian and 24% Ukrainian.