I can't specifically remember the problems with the rules themselves, but there was definitely a problem with the metagame. To illustrate (and this is all from memory mind, I haven't seen that set in almost a decade):
Imagine you've gone through 36 levels of play (i.e. years and years of real game time, assuming you didn't cheat and skip a bunch like most everyone did) and become a Paragon (or whatever is the deity-seeking titled for the class you've joined) performed all those mythologised and technically impossible tasks and succeeded. Your character feels on top of the world, with almost no equal, and if the campaign followed the spirit of the Masters set, probably deserves it.
What's the great reward for all that? Technically you're an immortal, but for all intents and purposes you're a nobody again...a little fish in a big pond again with puny powers, crawling up the ladder...again. You'd have been better off starting a new campaign from 1st level, as at least those adventures opportunities are more fun....or at least, that's what everyone who I know who read the set assumed - there was no real bait to make you want to play it.