I like something about all of the Mega Man games that I've played(1-9, X-X8), and I prefer the original series. It's mostly about the atmosphere, and the over the top "Insert verb here"-Man. The X series is cool too, and the upgrade armor is good stuff.
However, if I had to pick, I'd say MM VII is my fave game in the series. It's got a halfway decent story, Bass, good graphics, and a few secrets. Plus, the Rush Jet Armor makes it's triumphant return from MM VI. The only downside is that Wily's final form can be a tad frustrating.
Following that, I gotta admit that MM X is most definitely a polished game, and if it wasn't for my partiality to the original series, it would probably be #1.
Unfortuneately, after X3 we get a major decline in quality for the X series. X4 is ok, but it never really reaches the same level of quality the SNES titles gave us. X5 was too easy and boring, X6 had frustratingly cheap deaths and uneven diffuculty, and X7 just...doesn't work.
X8 though, that's where things shot up, cause it's awsome! I've only played through it once, so I'm not going to put it on my list as a favorite, not yet anyway.