Personally, the only major problem I have is with the fact that at mid-high levels, save or dies (which I dont really mind in themselves) become one of the only mechanically viable offensive magical options.
I dont mind creatures being totally immune to certain things, if its in line with their mythical/literary origins and/or nature. Fire Elementals for example should be totally unharmed by fire and heat.
I also dont think such resistances and immunities should be able to be overcome in the case of creatures who are composed of that element or energy or otherwise have it as part of their engrained nature.
However, having all Fiend types be immune to 1 or 2 energies, and resistant to 3 or 4 more is a bit excessive. Part of this problem is due to the Fiend groupings (Baatezu, Tanar'ri etc) all having the same set of defenses. I think each demon/devil whatever should have its own set, and usually perhaps 1 immunity and a couple of resistances.
I also have a bit of a problem, mechanically and conceptually, with Golems "magic immunity." They basically have unbeatable spell resistance against all spells subject to SR. And yet they are basically just animated statues.
A lot of the problem at mid-high levels lies in so many creatures having good saves, lots of HPs, SR and energy resistances all at once.
I think in some ways I'd like to see more creatures with specific immunities/resistances/save bonuses, and full blown Spell Resistance saved for fewer creatures with a more specific anti magical nature or the like.