All in all, I'd say these are pretty good rules. I don't think any will hurt your game, and some I really like to the point where I might use them some day when I can run a game again. A few I'll comment on:
- A player chooses at character creation whether to use Dexterity or Strength for determining attack rolls. Likewise, a character chooses whether to use Strength or Constitution for Fortitude saves, Dexterity or Intelligence for Reflex saves, and Wisdom or Charisma for Will saves. These choices can never be changed.
This is interesting. I've seen it suggested in one of my balance threads. Persoanlly I don't think I'd use it, but it really helps reduce MAD in some characters.
- Fractional BAB/saves will be used
It's really too bad this wasn't implemented in core. I can see why they didn't do it, but it's so helpful. I remember a player in my last game who wanted to make an Ultimate Magus. He picked up his PrC at level 6, and his build was Beguiler 1/Conjurer 3/Master Specialist 1/Ultimate Magus 1. That 6th level PC had a BAB of +1! Had I been using the fractional rules, it would have been +3.25 (+3 for game purposes). I know that's an extreme example, but still, good choice!
- Effects that grant immunity to certain effects now grant a +20 bonus on the appropriate d20 roll (or a -20 penalty, depending on the circumstances). The exceptions are Mind Blank, which grants SR equal to 20+Caster Level against mind-affecting spells and divinations (even if the spell ordinarily wouldn't allow SR for some reason), and True Seeing, which now grants a Caster Level check at a DC of 5+Opposing Caster Level to penetrate illusions. Racial immunities are unaffected. Energy immunities still apply against damage from energy; the +20 applies to appropriate d20 rolls against nondamaging energy effects, such as a Pyrokineticist's Heat Death (effects that deal both damage and have an additional effect use both rules). Being Mindless still grants immunity to mind-affecting effects, however.
I'm doing something similar in my balancing threads, although I hadn't applied a blanket rule yet. I think I was using either a +/- 10 or a +/- caster level for the modifier.
- Damage Reduction applies against crushing and falling damage.
This is smart. I don't think I've ever thought about that, although it's never come up in my games either.
- A character can forgo using their spell resistance for spells with the (harmless) tag.
If you have to blow a standard action to drop SR, this will be handy as hell.
- Death By Massive Damage does not exist. If the attack were really that powerful, it would have killed you anyway.
I've always hated that rule too.
- Homebrewed material will be allowed on a case by case basis. I am more likely to allow it, but only if it is well done. If it is under or overpowered I probably won't allow it (to protect you and my campaign respectively), but will allow you to fix it up if possible. Also if the design sucks (re: fighter-esque) I won't allow it, but again will let you fix it up. Heck, I'll even help if possible.
This is cool that you're willing to work with your players like this. I remember making a PrC for a player at her request, and she was quite pleased with it. I'm not sure she would have wanted to create it on her own anyway, but still, this sends a strong message to your players. It lets them know that you value their input to the game. Nicely done!