I won't address here the complaints of the rioters in Bosnia. Addressing corruption is mainly hard work: both keeping up the pressure in individual cases and pushing for structural reforms. Instead I will focus on Bosnia's state structure and its potential for reform.
As I have written before the main problem with Dayton is not that it provides safeguards for minority rights - that is just a decent thing to do in view of the hatred remaining after the war - but the fact that it is done in a different way for the Serbs and the Croats. That creates a situation where you have three parties with three different interests.
In my opinion the best way to reform Bosnia is to partition it in six provinces: one Croat majority, two Serb majority (focused on Pale and Banja Luka) and three Bosniak majority: (one centered on Sarajevo, one centered on Tuzla and one composed of Bihac and the Bosnian Krajna). Having more than one Serb and Bosniak province will create a situation where those provinces have different interests. So a conflict between provinces will not automatically be translated into an ethnic dispute.
Those provinces should have considerable autonomy: one should look at the Swiss cantons for ideas. Such decentralization can also reduce corruption as it puts the decisions closer to the citizens.
One shouldn't be too strict about the borders of those provinces. This is not a preparation for a partition. So one shouldn't gerrymander the borders too much as that harms government efficiency. Instead one should try to balance the number of people of a nationality within "their" provinces and those outside so that - if there ever might be a partitioning - you can have an equal exchange of territory.
The three headed presidency should be abolished. The ethnic veto should instead be entrusted to the provinces. When two thirds of the parliamentarians of the provinces of one ethnic group declare themselves against a proposal of the central government it should be considered vetoed. For this purpose those parliamentarians should considered in function as long as their successors haven't been elected. So dissolving a provincial parliament would make no difference. The governors of the provinces would have the authority to hold up any decision of the central government for a week so that the provincial parliamentarians have time to organize themselves. To diminish the reliance on politicians there should also be the option to have a referendum. Again a two third majority of the people living in the province(s) controlled by one ethnic group would be needed to torpedo a proposal.
By having the veto power assigned to the provinces one won't need any reference to ethnicity in the constitution.
In the area of education there should be more freedom and more efforts to have things in common. Pupils should learn at least some of the things that the "others" learn and they should also read some literature from the "others". Efforts to maximize the differences should be ridiculed - as they deserve.