Yeah, I've had some problems with hotlinking. Mainly with ancient wallpapers I made back in 2001, if you can believe it! Enough is enough, says I!
Sorry for bumping this up, but to answer this question, from the screens you've shown, the answer is two.
1) You gotta understand that cell phones come in different sizes. Hence the difference between the first two screens you're showing. You can see that the picture of Megaman isn't different, it's just adjusted to look good in different sized screens. Those really small and kinda neat (IMHO) graphics were for phones with very limited graphic ability. So the other one from 04 belongs to the same version of Rockman, just for a different sized screen.
I suppose you might call them different versions, but the code behind them is likely the same. Only the graphics have changed, to allow for the best resolution in the different sized phones of the day. Nowadays phones are much more powerfull, which is why you don't really see compressed sprites like you did for Rockmans 1 and 2 back when those cell games first came out. I haven't done reaserch on the subject, but the other classic games, at least, just might have compressed versions for them. But I can't really say for sure.
2) I don't think you can rightly say the Japanese version is truly a different version than the english. Again, you may technically be able to, but it's really just a matter of some sprites and words, so ...
3) Now the 2007 version IS a totally different version where you can unlock Roll. I think the Wily levels are preserved for this version as well. Actually, I wish the sprites for this version were available .... and maybe an emulator too ...
Hope that helps!