My brother and I had been working on our own version of 3.5 for a while before finding out about Pathfinder and I must say that I'm impressed. I particularly like the artwork! I noticed the comments about starting hit points in one of the side bars and that you guys kept one of my problems with 3.5, DR. I realize that Pathfinder is inbeta tesriht now, but I figure I'll put forth some of my ideas to at least get some feed back.
The first idea I had that might make characters more survivable at early levels also tries to tackle one of the, apparently, major problems of 3rd Ed: Instant Death effects. The idea is to throw in Wound Points which are equal to a character's Constitution + level + other bonuses. Wound Points would only be lost when you loose all your hit points or suffer an Instant Death Effect. So if a character gets hit by a Finger of Death Spell and saves she might take 3d8 + Character Level in Hit Point Damage, but on a fail she takes it in wound points. I was also thinking that this could be used with certain attacks such as the Wounding enchantment and Level Drain (something I've hated since it came out). Instead of causing bleeding wounds or loss of levels, each attack might do a couple of Wound Points. I was also thinking that you could apply staggered to someone who is into their Wound Points as well.
The second idea replacing DR with something that keeps a monster tough but allows every one to contribute. Its very frustrating for people when a DM throws a monster that their character can effect, like a Rogue using a Rapier fighting a Golem with out adamantine. Even DR 5 can make the majority of attacks in effective. The idea to replace it was Toughness (the Feat with the same name changed to Hardy and gave 4 HP and 2 WP) which gives a monster temporary Hit Points each round. So instead of getting DR 5/ it might get Toughness 10 or 15 that everyone can effect but still has to wear through before doing any real troubling injury to a monster each round. A weakness to a particular effect might do an extra d6 of damage. To simulate things like a Werewolf's weakness of silver I was thinking Regeneration could prevent it from taking Wound Points from any thing other then silver or elemental damage and even if you do, if it has toughness 10, you need to wear through that the next round.
I hope these ideas might be of some help. Sorry for the long post.