Kosovo and Vojvodina either don't get votes on the Federal Council or they are raised to the status of constituent republic meaning that Croatia and Slovenia don't feel like Serbia is trying to control the entire council.
The difficulty in a "Kleinejugoslawien" would be that by removing Slovenia, Macedonia and Kosovo (the last of which could not happen peacefully), you would be increasing the proportion of Serbs:Non-Serbs, which would actually make conflict between Croats & Bosniaks v Serbs much more likely.
The real forces which broke apart Yugoslavia were predatory economic practices by the US Congress and the IMF which (in the former case anyway) had the explicit intent of regime change in Yugoslavia. There was no perceived need to tolerate the continued existence of the SFRY with the fall of the USSR.
This combined with scapegoating by desperate former-Communist apparatchiks who wanted to maintain control of their fiefdoms (they would rather be big fish in a small pond than vica-versa). This is strongly suggested by the frequent cooperation between Tudjman and Milosevic, particularly on the issue of Bosnia-Herzegovina.
To save Yugoslavia, you would merely need to remove the economic pressure, perhaps change a few peoples' career trajectories around, and voila. The assumption that Yugoslavia was doomed is a myth propagated in Western historiography which absolves the United States of responsibility. Because of general ignorance about the Balkans, this is accepted as gospel due to lack of knowledge to the contrary.
The difficulty in a "Kleinejugoslawien" would be that by removing Slovenia, Macedonia and Kosovo (the last of which could not happen peacefully), you would be increasing the proportion of Serbs:Non-Serbs, which would actually make conflict between Croats & Bosniaks v Serbs much more likely.