If you're going to make a multicart, MMC5 would be the wrong mapper. You'd be better off with one of the multicart mappers. See mapper 45.
I looked into mapper 45. The only problem with that mapper (which is probably the same for the standard MMC3 I would imagine), is that it only supports up to #$80000 bytes of PRG-ROM. I experimented with it, and the hardwired banks always load 0x7C010 - 0x8000F. And Megaman 1, 2, and 3 combined, easily surpass that.
If MM1, 2, and 3 were to be put into a single file, unless there is another mapper that supports a minimum of #$A0000 bytes, they'd all have to be MMC5 mappers.
Converting MM3 to MMC5 would be a piece of cake. The real work would come from MM1, in which case the whole ROM would need to be re-converted to CHR-ROM, and that's just something I do not look forward to doing. It was a pain in the ass the first time around. Granted, it would most likely be easier and faster for me if I were to do it a second time, since I've got the experience now, but it's not something I look forward to doing. CHR-ROM conversions are A LOT of work. I've done three of them already.
It would be nice if you could toggle between CHR-ROM and CHR-RAM during runtime.