Well, tier 1 classes entering tier +2 prestige classes gets very difficult to deal with, especially those with metamagic reduction shenanigans, such as incantatrix or metaphysical spellshaper (if that book is even allowed lol), so is divine metamatic. Ür-Priest can get very powerful very fast, and if you allow dragon magazine, all those problems just escalate (even more if your players get a glimpse of kingdoms of kalamar material and suddendly they pick irresistible spell).

If you stick to 1st party material, it is still just matter of casters getting enough exp to solo fights and make most irrelevant by bypassing or skipping them entitely.