AP mages deal more damage now, they just have to change builds to do so.
I go for CDR runes and Seraphin + Rod of Ages. With the tons of mana, you'll get about 100 bonus AP only with that, along with the high base AP off the items while never running out of mana. I personnaly always disliked Zhonya, and now it got gutted I have nearly no reason to build it (unless im against something like Zed).
It's tricky, since you have to rethink about everything, but AP magse arent as weak as I excpected them to be, I even feel like I do more damage now (With Zyra mid, and even Brand with Thunderlord's Decree (and not the broken Deathfire touch), Vel'Koz and Lux are still nice).
Also, with the adc's rising, those mages are geting stronger since they can poke well without fearing of retribution from something like Graves that could two-shot them. They also counter tanks that coutners adcs, since they can poke them down, with Liandries and Void Staff, also most tanks are builing armor to counter the adcs, so mages still can do tons of damage to them.