I'm sorry to say that we won't be "upgrading" the Soulknife. Changing the BAB not only breaks an easy backwards compatibility, but also redefines the role from skirmisher to front-liner. We want to emphasize the skirmisher part and perhaps leave the front-line concept to a Prestige Class.
We'll continue to use our house-ruled version then. D8 hit die, slight re-arrangement of when things like throw and multithrow show up, and a handful of bonus feats. When we use the soulknife, we use it as a front-line character in place of a fighter/barbarian/paladin/ranger. With PF it's entirely possible that a rogue could take the place of one of these. Why soulknife continues to effectively be written as the 5th party member I'll never understand.
On the topic of backwards compatibility, there's so little soulknife-specific material out there (ignoring Dreamscarred Press material which is easily adapted) that it's a non-issue in my eye.
Anyone else have any ideas, feelings about our suggested system for a per-encounter PP pool?
Meh. We've talked about doing things the easy way and simply let the manifesting class have fewer power points per day and let them refresh. Or the active/max pool as discussed above. Per encounter you've got 1/4 your PP. At the end of the encounter, you rest a bit and draw from your daily into your active pool so you're good to go again. Kind of like Tome of Battle martial initiators and recovering expended maneuvers.
Your suggestion of ML+Int followed by full-round autohypnosis checks seems like a mighty nerf. One augmented power per encounter followed by every-other-round manifesting what works out to not-quite their highest level power? Errr, no.