Bah. I think they ought to stay. These aren't things that seriously complicate the game in and of themselves, they should be fairly simple to handle.
The only things that make them complicated are 1) WotC's inclusion of too many bonuses, buffs, debuffs, and stacking/nonstacking effects that have no limits or anything to keep them from becoming a chore, and 2) the fact that WotC can't manage to bother with any serious effort to print a clear set of rules in the first place, and then stick to their guns rather than giving everything an 'ahh, just get it out on the market already, we'll deal with any problems later' stamp of approval. I don't know if this has to do with being part of Hasbro now or not.
The whole mess of problems with Polymorph in 3rd Edition stems from the same basic problems. No real limitations were included (Shapechange and such just further worsen matters). Especially since WotC removed the old chance of mind-altering/no-going-back when using polymorph, which would limit its potential abuse. Just as they removed the aging drawback from Wish, for example (and removed other aging magic). Rather than just simplifying and balancing such things (like, let's say Wish drains 5% of your base maximum lifespan each time you cast it; so if your max is 100 years of life, and by the time you reach 50 you've cast 10 Wishes, you're dead; that would solve the problem of elves and suchlike having no problem with aging magic). Not like some 9th-level/epic spell couldn't be added that allowed a chance of regaining some lost years, or an artifact to do so, something an adventurer would really want to quest for.
It really, really wouldn't be hard to figure out and set down a concrete definition for Dispel Magic, Antimagic Field, and such, including how Spell Resistance works (though I'd prefer it be called Magic Resistance again and apply to more than just spells). All the company really has to do is not ignore what they set down in the first place when they start making all kinds of new magical effects, spells, and whatnot for later supplements. Is it really all that frikkin' hard to look at the definition of 2 or 3 spells/abilities in the Core Rules before printing a spell or creature that might violate, obfuscate, or confuse the matter of how it should interact with said Core Rules effect? It's not like it's hard to identify which spells may cause such problems, since they'd have to be doing some unusual effect to be a potential problem with the Core Rules as written.
We really, really don't need 300 or 500 hundred spells or whatever in the Player's Handbook alone, so it's not like WotC has to try and cram clear rules text into the Core Rulebooks. Tricky stuff like Mordenkainen's Disjunction, for example, does not have to be in the core rules if it would take up too much space to explain properly (and really, it should just have a simpler manner of functioning). We don't need a dozen different spells to buff a creature's Strength score, for example; Enlarge, Strengthen, and one other spell would do it, for example, as in older editions, but instead we get all kinds of spells in the Core Rules that are just slight variations or different-leveled versions with more effects piled on. If you want a Bull's Strength To The MAX! spell, you just apply metamagic to a Bull's Strength, or use another metamagic feat to cast both Bull's Strength and Enlarge Person in the same action. It really wouldn't be hard to fix metamagic either.
