Mmm. I don’t think the difference between indies and AAA is as significant as you think, as most of the best practices are the same for both - it’s just that the failure modes are different.
You’re right that indie studios are willing to take more risks than AAA games, though - so most of the innovations in romance (including Bioware’s pioneering advances in romance sidequests in the West) come from the indies - but by the same token, 90% of indie output is shovelware, and much of their “romance” is either gimmicky or just a route to the adult content that they’re putting in in place of plot.
By contrast, you can count on an AAA game to be managed and designed according to a standard, which means that it won’t be slapped together with a month of effort, but the developers are at best not free to take as many risks, and at worst engineering decisions (in this case, game design) will be driven by marketing or corporate concerns. In the case of romances, this means some marketer’s idea of mass appeal, as well as a combination of women-for-fanservice and less actual sex (I admit to being disappointed by how Mass Effect’s sex scenes get less explicit with each game, though even the first one was hardly raunchy!).
And one element is not usually related to AAA/indie issues: the scarcity of M/M romance. That, from what I understand, is actually driven by internal studio factors; namely, most of the people working in the gaming industry outside of IF and visual novels come from STEM backgrounds, leading to straight white men dominating video game development. The brogrammer culture has left its mark on video game romance even in places like Bioware (where a certain degree of progressivism has always been part of their brand).