In all honesty, disregarding my nitpicks on X8, design and all that aside, what bothers me most is the shop. EVERYTHING is buyable in the shop. It sort of kills stage replay value. I remember when you had to FIND Sub tanks and heart tanks. It added more incentive for hidden areas and stuff. And whatever your views may be on having to rescue reploids to get chips, it at least made them a bit more of a challenge to get, and again, gave an excuse to go back to stages. X8's levels, or at least a few of them, were just forgettable... and sort of... I dunno, linear? bland? I cant quite put my finger on it. Also, The majority of the capsules were pretty badly hidden. Right in plain view, just taunting you. Not like other X games havent done that, but X8 does it for almost all of them. I DID however, like the touch of putting one of them in the intro stage, requiring a revisit to find it. That was an interesting usage of the usually one-shot Intro stage.
Other than that, I think X8 captured the 2D Megaman gameplay just fine. I cant speak for MHX or PU, although ive seen a fair few comparisons between PU and MM1. (mainly the [parasitic bomb] like grabbing onto ladders not quite working as flawlessly, weapons not going through walls, and that stuff)
But I dont think 2.5D Megaman is the problem here, we have all seen that it can work. 3D is the one that... well, gave us X7. Though to its credit it also gave us Command Mission.
EDIT: I also agree with Objection's post on PU's visual appeal.