To put it bluntly: the costs. Basically, everything relating to how XII went down put a bad taste in a lot of people's mouths and it was no different in Japanese arcades. XII failed to deliver on anyone's expectations, for the costs that were entailed. And then a console port was rushed out, which left Arcade Operators PISSED. For it left them stuck with arcade hardware that was sitting around, doing nothing, while people were happily going back to the UMs.
Oh, I could see that... The Type^2 is not cheap, and Tatio is not that known for quality control. So when SNK let slip a bad (obviously beta) game on the system and then rush to console, it would leave operators in a lurch. I would hesitate to buy direct from SNK again, unless they had gold on their hands ... lucky for them that XIII is the better game.
For much of the same reason, Capcom seemed insistence to keeping SSF4:AE to a 6 month window (much to Ono's annoyance), having SSF4 at home and SF 4 on cabs for a year wasn't pleasing operators any and AE was the push to win them back (alas, while making enemies of players/consumers here for the release of AE).
So much did XII change things for SNKP, that they had to make deals with Konami to act as the publisher for the arcade release of XIII. Likely done to make it so that operators felt that they had a little more "security" when it came to committing to another investment to buy the hardware.
Oh, that is bad. But that also explains why '98 Ultimate Match Final Round was made for NasicaLive. Just case XIII failed, operators would have something to look forward to and keep the cab running, something that I am sure they got an earful of when XII failed in the market.
So, yeah, the whole XII episode stands as arguably one of the "worst case scenarios" in this vein. Even so, I'd like to think that FB and Ecole wouldn't turn a blind eye to that much, seeing how UNIB represents their own first foray in HD, and that much of an investment is expensive as it is. Sega may be looking out for their interests, but FB, especially, has to be considering their own stake in their future.
This is part of the reason to why one manufacturer "to rule them all" is not a very good thing for a market. Basically, Tatio makes all the rules at the moment and if something fails... it does so hard and Tatio has no incentive to do anything about it. With Sega around with a few high profile games in the pocket, Tatio is forced to compete and keep games from failing too badly.
As to the Indie/Doujin developer trying to make it in, I would be hard pressed to say that it's good for them that the chooses remain narrow.
Well, as far as FB/Ecole goes... we'll see where they take the game once made. As much as I speculate, there are still a few things that would randomize what happens. Given the MBAACC 1.07 PC release with Carnival Phantasm, I am not sure what will happen (didn't see that one coming) with UNIB. That said, at worse it's an .EXE that they can dump on NasicaLive/ALL.net when they need to. And really, Sega does have a price advantage on Tatio with hardware... with that in mind, a good game to watch at the moment is Chaos Code... which happens to be a Ringwide-game, if response about the cabs are good then it would likely do a lot at Sega's end of things. And to be honest FB would have to be watching.