There have been a few news stories recently about language in Kyrgyzstan and Kazakhstan (there are always here, but I'm highlighting a few today). Roza Otunbaeva was reported to have said that she supports more Kyrgyz language instruction in schools in Kyrgyzstan with more subjects being taught in Kyrgyz instead of Russian. Another article was about Uzbeks in the south who support Kyrgyz being taught in schools instead of Uzbek. A third article was from Kazakhstan where two schools in one city were changing their language of instruction from Russian to Kazakh in the fall. Apparently hundreds of lawsuits have been filed.
I've written on this topic often. In some ways I am uncomfortable with Russian being the most common language of instruction in Kazakhstan and Kyrgyzstan; it's almost universal in the universities, although not completely. Russian is the native language of less than half the people in Kyrgyzstan (although it's not only the native language of Russians; there are many Central Asians who speak Russian more comfortably than Kyrgyz, for example). Russian is also best described as a colonial language in Central Asia. It also has great potential to replace Kazakh and Kyrgyz as spoken languages, although that isn't likely to happen any more, at least in all parts of each country. It also carries Soviet baggage with it. Some of that baggage is positive, but not all of it.
But there are some excellent reasons why Russian should be used. There are far more books published in Russian than either Kazakh or Kyrgyz, and students who are confident in Russian have much greater access to world literature. And even though Russian has its problems and isn't a neutral language here, it's probably more neutral than any other potential common language.
And there is a need for a common language. Kyrgyz (in KG, obviously) is in many ways a logical choice. The majority of the people in Kyrgyzstan are Kyrgyz, and a significant minority speak closely-related Turkic languages. But Russians and Dungans and Koreans especially don't speak Kyrgyz or anything like it and many would probably prefer using Russian rather than Kyrgyz as their common language.
I don't really think there are good answers to any of these questions. I wish it were easier to educate people effectively in Russian, Kyrgyz, and whatever the student's native language is (Uzbek, Dungan, etc) if it isn't Russian. That would be ideal, but it's not really possible. Compromises have to be made somewhere.