alexis, I agree with you. I wanted you to listen for yourself and not bias your opinion with that of my own.
I've already listened to Lady Madonna on my 1987 stereo, 2009 remastered mono, and 2009 remastered stereo CDs and do not find any difference in the clarity of Paul's bass. I personally think the "muddy" bass, as you describe it, lends itself to the song and was meant to be that way. The piano sounds honky tonk as well and I remember Paul once describing this song as his "early Elvis imitation."
So don't be too disappointed with this particular song as it appears in the rematered CDs. The overall quality of the remastered stereo CDs is a bit better than the 1987 CDs when you listen to them on a decent stereo system. The remastered mono version of Lady Madonna is nice, but it's the first time we're really hearing it that way.
It's still one helluva song!