It would be interesting to see how the rise of Islamism is affected. Along with the war in Afghanistan, the ethnic cleansing against Bosniaks, Albanians during the Yugoslav wars and the Chechen wars attracted an ideologically motivated core of "foreign" (just fellow Muslims in their view) fighters who saw themselves fighting in a clash of civilizations with the west.
If Moscow is less internationally prostrate before NATO in this ATL '90s, the US will be more hesitant to intervene in the Balkans or the Yugoslav crisis may evolve differently. Even if Yugoslavia manages to hold together, the nineties could still have a nasty separatist insurgency in Chechnya.
In the 1990s Tajikistan had a civil war that pitted old-guard communists against a rebel coalition of islamists and reformers, if the conflict isn't butterflied away it may appear as a separatist insurgency within the USSR.