mkv is more popular that you may think.
Over the last couple of years, pretty much everything has gone to mkv. Almost every video I get now is mvk, and no, I don't get any japanimation. (not that there's anything wrong with that)
Even on non mkv files, the PS3's built in media player is INCREDIBLY picky about which of my files it will play. Files that play just fine on my 360's player (which itself has a lot of compatibility problems), original Xbox w/XBMC, or my TV's built in media player will throw up "incompatible format" messages or even an idiotic "corrupt file" message when the file is clearly just fine because other players have no such problem. Showtime on CFW PS3 plays almost everything, though.
I wouldn't let media player issues stop you from getting a PS3, though. It's still a good system.