Let's Read The Immortal Handbook Bestiary

[JoshuaZ]

How? Since you can create Pun pun at level 1, is level 1 broken too? Is playing 4 level 15 fighters broken?

Pun pun requires a whole bunch of splatbooks and one specific badly written ability to work. That's very different than in-core broken spells and abilities.

Sure... call it that. But the point is the game only "breaks down" if you choose to, therefore it does not automatically happen, ergo its not broken per! You can play a low-mid optimized game and nothing breaks down!

This argument doesn't work at three levels. First, what people consider optimized varies massively from group to group or even within a group. Second, one of the more serious problems is that many of the most seriously broken things come from wizards, and wizards in-game the hyper intelligent people who are trying to break the laws of the universe. If an int 22 wizard isn't optimizing their spell selection, then they likely aren't roleplaying well. Third, in order to avoid too much optimization one has to cut out whole swaths of the game; I'm not convinced the level 15 claim is true, but certainly by level 21 the degree to which epic spellcasting can be abused renders many in game threats irrelevant. And epic spellcasting is a system where one is explicitly able to make new spells; note that if one restricts to the existing spells then the system is insanely weak and hard to use.

Our DM said many years ago, that all the tricks we used, any other NPC worth his/her salt knew too... So unless we wanted to fight Pun Pun... we should think carefully what we abused...

Is this something your PCs are aware of in game? How is this not functionally bad metagaming? "Oh, I could take Maximized Time-Stop as a spell-like ability, but if I do it, the Dark Lord might also" makes no sense.

EDIT: That saves increase faster than its possible to increase the spell DC, mages are actually becoming relatively weaker over time as they increase in level... That's a broken mechanic.

This comment suggests that you simply don't know much about how to optimize mages. First, this is to a large extent not true. Second, by the time you are high level, one shouldn't be targeting things which allow a save anyways.

I absolutely love 3.5 and PF but that doesn't mean I can't acknowledge that getting them to work well at high levels in a consistent way requires a lot of either rule changes or having PCs actively restrain their own choices in ways which stretch credulity.