No offense to anyone, but I wouldn't blame Paizo for this...I'd blame the DM's. As a DM you have to know what your players can handle, and what constitutes a balanced or tough encounter for them. (and when to recognize an impossible encounter).
Those over the top, very maximized, near impossible end battles can be easily toned down to a more appropriate level of difficulty.
Should they be tough? Sure. Should they have the potential for character deaths? Sure.
Should they be TPK with little chance of survival? No.
Agreed. And thanks for stating what should be the obvious, but sadly gets missed far too often.
I'm not going to sit here and say that 3.5 RAW isn't broken in some places. It is. And any adventure (AP or not) that includes higher level encounters are going to illustrate some of those problems. And I'll also conceed that in some Paizo AP's the power creep got a little heavy. Of course that's why as a GM I read & review an adventure and fine tune it for my group before I play it.
Having said that, any GM and any players who are not aware of the characters capabilities or the rules to the point that a combat which lasted for only 4 rounds took hours to play, needs to get some help.
I know this is based on personal experience, but I never had a problem with the combat time of my 3.5 games. The players all knew that they had a limited time (1-2 min max) to make their decision and take their actions. And as a GM I was on top of all the NPC's and if there was a question about the interpretation of a rule, I made the call at that moment and then reviewed it after the game was over. With those few simple guidelines, even boss fights usually took less than an hour.
If I can run a game that way, I really don't see what is preventing others from doing the same.