While we can't blame Paizo for 3.5 flaws, can we blame them for blindly adhering to what are clearly problematic rules and further propagating them?
For example, if we know that high lv npcs are too weak for their cr, why then do we still stick with them, and list fighter18s as cr18 (or worse, some funny, completely unoptimized combination such as fighter4/wiz7/blackguard4 as cr15?). Should the designers not take it upon themselves to ad-hoc some changes (and maybe address them in a tiny sidebar, so we know they are deliberate, and not some kind of oversight). Maybe if they wanted a mindflayer wiz7 npc, take the initiative to revise its cr to a more resonable 12-13, rather than cr15.
If we know that certain encounters are undesirable due to all the logistics involved, then try to reduce/do away with them altogether, rather than flooding us with the need for endless grapple checks and the like. If statting out high lv wizards is tedious due to the need to account for even cantrips, then maybe stick with sorcerers or simply handwave away all spells of 5th lv and lower (and say that they are food for arcane fire or versatile spellcaster or something).
Play up what is so desirable about high lv play, while down-playing the undesirable bits.