I'm curious to see if monsters overall will be stronger in the Bestiary.
Overall, I think the Pathfinder classes appear stronger than their 3.5 counterparts. Will monsters be scaled up to match?
In some cases, the monsters will be weaker; in others they'll be stronger, and in some they'll be pretty much the same.
One of the big things we did when building the monsters for the Bestiary was to create lists of a lot of benchmakrs. "How many hp should a CR X monster have? How much average damage should it do in a round (and thus how many hits does it take to ruin an average fighter of the appropriate CR). What's the average saving throw, and how should it match what an expected PC save will be? What AC should it be for each CR to make it so that the average high BAB class like a fighter can hit it often enough to make sense?"
Lots of different numbers. We figured these numbers out for every CR, from 1 to 20, and then made sure that each monster falls into these ranges depending on its CR. Most monsters will have one category that they stand out in; a tyrannosaurus, for example, might do more damage than it should for its CR, while an ankylosaurus would have an extra high AC or maybe more hit points. But overall, the charts were a GREAT service to us in making sure that all monsters of a specific CR are roughly in the same ballpark as far as hp, AC, attacks, damage, saves, and ability DCs are concerned, and these values were determined by what the average PC would be able to deal with for that level/CR matchup.
In the end, since we made a conscious effort to make sure that no CRs changed so that adventures in 3.5 won't need to have lots of monster substitutions if you play them with PRPG, this DOES mean that some creatures got nerfed. Apes are a great example, since they already did a lot of damage for their CR and on top of that had a rend attack, which is basically free damage if they hit with their claws. We ramped back their damage so that they're still a bit high for their CR, but not so high that they'd look more at home on a creature that's 4 or 5 CRs higher than this (girallion, I'm looking at you!). In other cases, like the rakshasa or the ogre mage, they were far too wimpy for their CR scores and we gave them a significant boost to their abilities so that their stats would make sense for a CR 10 or CR 8 monster. And in a rare few cases, a monster in the SRD simply didn't work at its 3.5 CR and we simply had to bite the bullet and change its CR.
In any case, all of the guidelines and rules and benchmarks we used to build the monsters in the Bestiary are included in the Bestiary's Appendix 1, so GMs can use the same information to create new monsters of their own using this same method.