I think it would be a good idea it would be a lot more competitive and if it was done correctly it could break the duopoly in Croatia and Serbia (Dinamo Zagreb and Hajduk, Partizan and Crvena) and even then these duopolies are turning into monopolies, which would benefit both countries in the long run. It's hard to talk about duopolies in Bosnia (because for many years it was run as two seperate leagues, and Montenegro (since it on seperated from Serbian league 5-6 years ago).
There would be a lot more international interest in this league. For a start it would be a higher standard, it would be more unpredictable (as to who wins). Also in terms of abroad, there are quite a few countries with a lot of expatriates of from all of the Balkans - countries like Germany, Australia, Canada, Holland, USA (Chicago) if you had a merged ex-Yugoslavia league it would be a lot more likely to get coverage in these countries. If you for instance show the Croatian League in Germany you have a potential audience of 225,000, but if you have the unified league (with Bosnia, Serbia, Macedonia, Montenegro) you have more like 700,000 - so from a German TV Stations point of view the merged league is more attractive to broadcast. It might mean that clubs could keep the players a bit longer and get a little stronger in European competition. The best players will probably always leave, but maybe they could go from a Balkan club direct to a great club. For instance maybe Dzecko could have played locally instead of 2 years in Czech Rep, Mandzukic could have stayed at Dinamo Zagreb an extra year, skipped Wolfsburg and gone direct to Bayern, maybe Ivanovic and Vidic could have gone direct to Chelsea and Man Utd instead of via a couple of years in Moscow, maybe Sulejmani could have played a little domestically (instead of Heereenveen), likewise Pandev could have skipped his first spell at Inter (where he was just loaned to lower league teams in Italy) and gone direct to Lazio or Napoli.
As I see it the only major downsides are possible crowd trouble (which sadly I think would be likely at first) and problems getting into European competitions. But I think there are ways around both of these issues. I would close the fixtures to away fans (from the different republics) for the first few years and then gradually re-introduce away fans for some fixtures, and then when this has been ok, re-introduce away fans for all fixtures. So using Dinamo Zagreb as an example fans in the first season can go to away games against NK Rijeka, Hajduk, Osijek etc, second season Maribor, Velez Mostar, Vadar Skopje, and if that's ok then to Partizan and Crvena Zvezda (and the same rules for Partizan fans).
The problem with European football qualification is that you could end up with a situation where only 1-2 clubs in the merged league are ever close to making CL or EL group stages. So it could be Partizan and Dinamo are the only teams to get close to the CL for decades, and others like Željezničar dont even have the chance to make Europe. It's something that could be a problem in the proposed Ukraine-Russia merged league (potentially you would only have 1-2 teams of Shakhtar, Dynamo Kiev, Zenit, Spartak, CSKA, Anji getting to the CL whereas at the moment 4 can) - the organisers of the Russian-Ukraine merger are trying to get UEFA to stagger the EL/CL qualification for 4-5 years to make this less of a problem. So for the first few seasons, the top two Ukrainian and top two Russian teams would make the CL (even if say only Russian teams finished in the top 4). I think they could do something similar for the first years of a combined ex-Yugoslavia league, and then run European qualification normally.
