The Master System is the version I've spent most time playing, and my only real criticism is the lack of difficulty.
There are some levels - like Just a Minute - which are waay too easy for their position. Others are fairly difficult, but there are no levels which stand out as being difficult enough to cause major problems.
However, the challenges presented in trying to 100% levels make up for this. Between us, Pooty and I have managed to 100% nearly all the levels (although he's done most of the harder levels!).
The gameplay is so much smoother than the NES. There is a little bit of lag from time to time, but nothing to cause major issues.
The pause button's position does cause issues, and quite often, the game will crash when you're fumbling for the pause button, but that's a flaw with the Master System itself.
I'd like to add the SEGA levels to the mix of ridiculous levels. SEGA ONE, SEGA TWO and SEGA FIVE are all pathetically easy (especially seeing as these are all repeated in Mayhem with very little change to the solution). SEGAs THREE and FOUR are a little bit harder, but they're still not difficult.
I do like how the Master System has its own set of glitches.. its glitches are pretty fun to exploit. There's a great glitch which can turn fire on the ground into terrain, and another glitch which allows you to build on the flamethrower.
But, if I had to pick an 8-bit version to play, it'd be the Master System version.