Regarding Skullgirls (from memory):
-Game is released to a pretty positive reception
-Game has some bugs, some balances issues (ALL 1st release FGs have balance issues) and a few missing features
-Developers (a main crew of like 15 or less people mind you) are working to addresses all issues and would have done so super fast EXCEPT
-Their publisher (Autumn Games) gets sued by Konami (that company Jim Sterling rails on weekly for being shit) over a completely unrelated game (Def Jam something or other) the two worked on together.
-This results in all of Autumn Games assets being tied in the lawsuit. Which means they can't pay the developers who are thus let go
-With no money or office the developers plug away at addressing all the issues (with NO PAY) but can't actually update the game for like 6-7 months (as reception cools and other games come out). Developers are forced to essentially form a new studio (Lab Zero)
-Microsoft being especially difficult to work with and some peculiarities with XBLA make updates on XBLA drag behind the PSN version
-With no money they can't add new material to the game
-After a very good run at the EVO donation drive, they try a IGG campaign
-Campaign is very successful and after like over a year they finally have money to add to the game (Autmun and Konami suit is still going on)
-However as Konami also helped publish this game, they still have to go through Konami to update the game and Konami, unsurprisingly, proves to be super inept and makes things difficult and updates slow.
-They were able to get the game published in Japan by Cyberfront who publishes a lot of Western games. Game sold more in two weeks than the JP publisher expected to sell ever. However, Cyberfront went belly up which forced the developers to get a new publisher and got the game taken of PSN for a while.
-PC version funded/published by Marvelous and I think that has been mostly drama free. No idea what the contracts for that looked like.
-Eventually, they sever ties with Konami but not before the later throw a few jabs their way (like getting the game delisted from PSN/XBLA for a while)
-Autmun and Konami lawsuit only recently ended (which I assume is where they got the cash to do a PS4/Vita port)
I think I hit everything? For an indie game with a new IP (only 1 of what 3? new fighting game IPs this entire gen released in US) reception and sales have been fine as far as I can tell (near 100k by the end of 2012). But yeah, like a TON of problems crept up that had like nothing to do with the quality of the game or the competency of the developers (who have been exceedingly hard working and open with regards to communication - CEO of Lab Zero regularly posts on GAF and I know Mike Z talks with the community all the time)