Max this is a great idea. Here are some thoughts I have on this...
Minimalist
-cultural autonomy within the Federation or within a centralized state devoid of entitiesOn paper this sounds like a good option. In theory Croatians would be able to organize schools, media, etc. If it is a centralized state well we might have eliminated an obstacle (the RS) that keeps Croats from returning to their pre-war homes.
Having said this, I do believe there are dangers present with this minimalist plan and that these dangers outweigh the benefits that this plan would have for Croatians in Bosnia and Herzegovina. Cultural autonomy does not equate to political autonomy. Minimal for Croats is maximalist for Sarajevo especially if it involves centralizing the government structures of either the Federation or the whole country.
I would even go so far as to argue that out of the three options given this is the one most appealing to Sarajevo and the one that they are trying to implement in their own image right now. We see that with the loophole in the election rules that let non-Croatians elect people like Željko Komšić. Then they can say “look the Croatians have rejected nationalism,” etc and try to have the SDP (and Sarajevo) set the agenda, and not the Croatian people themselves.
I also cite as evidence the recent discussion of a Croatian language television channel. The response out of Sarajevo was something like “they don’t have that many journalists” which basically for us translates into “the Croats are illiterate goat herders living up in the mountains and must nurtured by the highly educated and cultured people of Sarajevo”.
The result of this would be, at least according to Sarajevo should this somehow succeed would be that they would choose the leaders of the Croatian people and try to erode anything that resembles Croatian identity in Bosnia and Herzegovina and then parade around “Bosnian Catholics” for Easter and Christmas and say “see we’re tolerant of everyone”.
Finally, considering that the “highly educated and cultured people of Sarajevo” were dumb enough to get themselves surrounded in the war, to me means that they are not competent enough to run the country, much less to decide what is in the best interest of the Croatian people in the country.
Median
-3rd entity either de facto or de jure carved out of Federation territory or even through land-swaps with RS, the Mostar question and its effects on other cities like Travnik, territorial continuity vs. discontinuityThis is the one I most favor and I favor a model of discontinuity, because it takes into account that Croatians in Bosnia and Herzegovina are not concentrated in one area. The pros with this model are that we can be surgical with what can be a part of it and not worry if it is connected. If land swaps can be made with the Republika Srpska we can get certain areas that we feel are important for the development of the entity, either by the potential for returnees or for strategic value.
- This model works well in other places like Switzerland. Several cantons within the country are not contiguous like the Canton of Solothurn:

- This model works well in Moldova where the ethnic Gagauz people were given a wide range of political autonomy and the territory is not contiguous and is majority Gagauz:

- Finally this concept is not exactly new to Bosnia and Herzegovina either. The Federation is not contiguous, and the Posavina Canton is both separated from the rest of the Federation, and it is made up of two pieces. Technically neither is the Republika Srpska as the Brčko district cuts it into two pieces.

The big issue here is that this plan doesn’t happen in a vacuum and your big issues would be trying to sell it to Sarajevo which wants to be more centralized, and would not like to see any form of Croatian self rule, especially in areas like Soli, Travnik, Kraljeva Sutjeska, etc. Territorial swaps would be a tough sell, but not impossible with the Republika Srpska. I think they would be OK with offloading areas like Stjepan Krst or Komušina, but would be leery of ceding areas of Posavina because it might endanger their aspirations for independence and or if SHTF…
Maximalist
-secession and annexation by RH (in a SHTF scenario where the state collapses and the global leaders allow for it to fall apart) with respect to what should be secured and what should be left outI think in a SHTF scenario all bets are off. I know what I would do, but I think in this scenario Croatia needs to be mindful of its own security as well. I do think a collapse in Bosnia would impact Croatia as well. I think Croatia's southern flank is a security concern especially if I am correct in thinking that if Montenegro were pulled in the Serbs might make a grab for Boka Kotorska...