It was also the decade when there where less gaming related options on PC especially since USB hadn't been invented or taken off for most of it. At one point the best you could do is get a sidewinder gamepad or a gravis gamepad and hook it up to the sound card which only had one port so you either had to have one person play with the keyboard and the other with a gamepad, share a keyboard. Or you needed to get a gamepad that could daisy chain to that one port and have a game that specifically support it.
Many of the PC fighting games in the past where for DOS which didn't give you very good controller support. Good controller interfaces just weren't there yet for the most part. They hardly even had good graphics API support much less controller support back then.
Also there weren't as many viable display choices for the PC. Back when midway did MK1-4 on the PC most people where limited to just a 14 inch or below VGA CRT monitor where at the arcade they had a 27 inch RGB CRT monitor in the cabinet. The VGA monitor gave better colors than TVs of the time but where too small to crowd around to play two players pretty much.
Nowadays not only are there much larger available monitors for the PC but thanks to modern display tech in HDTVs they can easily be used as computer monitors too. In my living room I have a PC hooked up to an HDTV and I've used it to play PC games including fighting games with a USB controller just fine. I was playing KoFXIII just the other day on there with my fighting stick. Even my main computer has a big 16:9 display now.
Nowadays controller support is a lot better especially since one can easily hook up more than one controller of their choice which could be just about anything from the 360 controller, to fighting sticks, to adapted classic console controllers, etc. Apparently many people today fail to realize this.
Simply put pretty much all the technical reasons the PC fighting game market may have been held back in the past are now gone. So saying they gave the PC a chance back in the 90's is like saying someone gave commuting a chance when horse and buggy where the main way people traveled and they didn't like it so they don't want to give cars a chance because they think they'd have all the drawbacks of horse and buggy.
Also, nowadays fighting games mostly use engines that where made first on PC such as Unreal Engine 3 for MK or the engine Capcom uses for the new Street Fighter games. At the arcade they are actually made for and run on standard PC hardware using Windows XP basically. So, technically speaking it's easier now to port those to run on consumer PCs than it was in the past where they used custom hardware and engines written specifically for them in assembly.... combined with the fact that they didn't have the type of software and hardware available to them now.
Seriously... they are making arcade machines which are PCs under the hood now.... the software\hardware is even standard enough that the games from them can be run on off the shelves PCs with little modification.
Mostly the PC just has a bad rep or a perception problem when it comes to fighting games due to outdated beliefs surrounding it like I mentioned above. Like people saying "Uh, why would anyone want to play a fighting game with a keyboard?" as if it'd be the only choice.
The only thing that can be held against the PC is perhaps less people would buy the games although Capcom apparently have found a market. Like I've said elsewhere I'm sure Capcom isn't releasing their games on the PC as a charity.
