I think an earlier embrace of market reformism would help. Or quite simply not having Milošević. Milošević came to power through the anti-bureaucratic revolution where he replaced the soft-nationalist and/or reformist leadership of the Serbian Communist League and then proceeded to replace the Kosovo, Vojvodina and Montenegro leaderships with loyalists (giving him a majority in the Federal Presidency).
He also deliberately undermined the deflationary policies of the Ante Marković government just when they were starting to work. It would help if Marković also had created his political party, the Reformist Union of Yugoslavia earlier - that way it would have created a Yugoslavist party that was not the post-Communist social democrats. If perhaps Marković was also able to convince the leaders of the federal republics to allow him to organise democratic elections at the federal level, that'd be of great help to legitimise him. Not sure how to do that, though.
Another angle is the Croatian electoral campaign going differently. For starters, the Communist leadership could be less sure of its chances and not implement a single-member two-round electoral system. If instead, they had introduced a PR system as the democratic opposition parties had demanded, Tuđman's victory would not have been anywhere as crushing (60+% of the seats with 41% of the vote). I think this very different electoral dynamic would have helped divided the anti-communist vote further between Tuđman's HDU and the soft-nationalist/liberal Coalition of People's Accord (KNS) led by Savka Dabčević-Kučar [1].
Another one is that the process of Serbianisation of the Yugoslav National Army could be avoided.
[1] Who was actually the first female head of government of Europe as President of the Croat Socialist Republic's Executive Council from 1967 to 1969.