Pathfinder should not be mixed with 3.5 unless you really, really know what you're doing. Many of the gaps in 3.5 such as divine metamagic and all purpose druids have been closed.
I would advise consulting with your players and restarting the campaign with ONLY pathfinder rules. If you're really concerned, limit it to the basic books.
You can agree to let any player that wants to use XXX PrC/feats/etc use those stuff with an open caveat, that you will work with the player to balance out any problems that occur during play (aka its overpowered) or remove the PrC and let the player rebuild his character. Just remember to inform beforehand and make it fair if something gets removed
Alternatively, just roll with it and let them overrun your monsters (remember you're not really aiming for a TPK). Or dump in a lot of weaker monsters (or summoners with stuff pre summoned) and swarm which will force more resource usage. Or use harder tactics vs the party (however this may kill them if they don't know how to handle it) such as incorporeal flyby attacks from below the ground, flight based encounters, magic jar attacks etc
Regarding magic users from 1e, 2e and 3e,
In 1e magic users only became powerful once they hit level 10+. Save or dies were of no consequence because it was simply so easy to save (qv old save tables and a XXX of protection so failure was only on natural 1). Because of the way HD was handled, it was easier to simply spam damage. At lower levels, you could die easily because your AC and hp was really bad compared to monster THAC0.
20th+ level casters ruled all, not because they used save or dies but because they used magic w/o caps at range, ala 10 auto hit magic missiles per casting for 10d4+10 or the 20d6 fireballs that made meteor swarm a less than spectacular spell. You really had no chance at mid levels if a high level mage BBEG telported in.
Classes no longer had hit dice after a certain point wizards at 11, fighters at 9th, etc so they did not have sufficient hp to take large scale 20d6 hits. The 88 hp huge ancient red also was just free xp against uncapped magic as long as you avoided immunities
2e closed the magic cap problem by limiting the maximum level effect. This weakened magic users (renamed wizards or mages IIRC) a lot and save or dies still were useless (qv the same tables again plus the same XXX of protection).
Added to TWF and the player option range of grandmastery, at 7th level (you could find the slots but it was not easy), the fighter was actually the most powerful single target combatant. The main problem was WP slots (rather like the feat deficiency for fighters in 3.5) but that only delayed the ridiculous power of the fighter. A optimised TWF grandmaster fighter could take down an average (non maxed hp) great wyrm red in 1 or 2 rounds even with the changes to dragon HD from 1e, by using twin longswords 4x(d20+3+3(+3 magic weapon)+6(18/00 strength)) for 4d20+48=~90 damage/round.
Consider that the average 20 HD monster had ~90 hp and it become LOL. Of course if you had twin vorpal weapons, things normally ended even faster since you spammed for the successful roll range 4 times every round.
Compare vs the 10d6 fireball that would need a 10th level+ magic user to cast and did an average of 35 damage, wizards became the mook killer while fighters were the boss killers.
3.0 was a revolution so everything was very different. The whirlwind bag of rats fighter was invincible as long as he had rats and after that was FAQed, grabbing feats and PrCs to stack Spell DCs became the big thing as that old save table was no longer in use. Save or dies became top dog until epic spellcasting made everything LOL.
3.5 reduced that issue by halving all spell DC gains and in the cases of PrCs, changing the spell DCs to caster level increases. Save progression lag then became the main issue as spellcasters compensated by targeting weak saves. Of course stuff like divine metamagic and such were around and stuff like lion totem barbarian 1s became available. Epic spellcasting was not talked about much that edition, as it was stuffed in the secret closet and many hoped it would remain unnoticed.
An interesting point is that the very rarely referenced but common break point across all editions (though it has greater or less costs in each edition) and even pathfinder has always remained the same. Simulacrum.
