The thing is, when we use something like 2xSai as a post processing filter, sure, it makes faces and other details a mess.
But the developers can run the filter on their original sprite data, and then get their artists to clean up / redraw the faces and other small details. (so the filter is not actually running in-game.) It would still need a bit of manpower to do it, but only a little, and nowhere near as much as redrawing everything like KOF12.
Especially for a game like MB, where the characters have large areas of colors and clean lines, I think running the sprites through a filter (and then cleaning up where necessary) would work really well.
It's a shame that MB is quite nice graphically, but the sprites are just so blocky due to their age. I was hoping they'd do something about it in MBAA.
In many ways, games like KOF98 dont seem as bad (or maybe I'm just so used to it) because everything is at low res. But MBAC's low res sprites on higher res backgrounds look rather jarring. (same with KOF98UM on PS2 with the 3d backgrounds.)
Again, I really wish they'd discover 2xSai already
Used carefully on their original sprite data (rather than slapped on afterwards in the game code) it can do a lot of good imo.