Recently visited said museum and was a bit disturbed by it. It mostly focused on the period of Lithuanian history when it was a part of the Soviet Union as well as the Lithuanian nationalist partisans. There was little mention of the Holocaust and nothing to indicate that Lithuania was a particularly unsafe region for Jews nor is there any mention of Lithuanian Jewish partisan. One display actually mentioned the Lithuanian nationalist partisans as having a strict system for internal discipline and court martials but stated something along the lines of (paraphrasing) mistreatment of civilians did still happen as it does in all wars.
I guess I'm just wondering what current scholarship thinks of this kind of public history. I found the whole thing quiet distrubing as it seemed to present a kind of dual genocide thesis where Soviets were the more vicious perpetrators while also distinguishing between Lithuanians and Jews as if Jews did not count as Lithuanians. Is this considered by historians as a form of Holocaust denialism?
Oh, a question about the building I'm living next to :)
On your visit you should have noticed that the building itself, where the museum is now based, was used as NKVD and latter KGB headquarters during the era of the Soviet Occupation. The names carved into the wall stones are those of people who were imprisoned and murdered there - mostly members of the independent Lithuania government, intelligencia and resistance fighters. I think it's befitting that the museum concentrates mostly on the Soviet crimes, as this was the place were these crimes took place. To be astonished that it is like that would be like going to Auschwitz and wonder why there's no mention of Soviet crimes against the Polish.
If you would like to learn more about the genocide of the Jewish population, I would suggest visiting 9th fort museum near Kaunas. This museum (much bigger) has emphasis on the Jewish victims of Lithuanian population and Holocaust, http://www.9fortomuziejus.lt/?lang=en
Over 45,000 jewish people (and other too) were killed there, so for obvious reasons youd only find limited references to the Soviet crimes.
Or, if staying exclusively in Vilnius, you could visit the old Jewish quarter, just a half hour of light walking away from the former KGB headquarters, and check out National Vilnius Gaon Jewish Museum on your way there, sorry no English website version jmuseum.lt