I've followed Rycanada's various E6 threads, here on Enworld, for over a year (maybe longer). I'm really a fan of the idea.
That said, I'm wondering why you've chosen to include an ability increase progression, bonus skill points, increased maximum skill points, defense bonus, etc... instead of just using the one feat per 5,000 XP that Ryan originated the system with?
One of the primary things that come to mind is that (it seems to me that) you've actually increased the speed of gaining skill points and ability increases after 6th level when compared to the standard Core 3.5 progression.
Another thing that would bother me is the idea of increasing the skill point cap based on the bonus levels. One of the hallmarks of E6 that I really liked was keeping what an epic character could do closer to the realm of the real world. Part of the reason that sixth level was selected seems to have been based upon comparisons between maximum skill points at 6th level with real world records in various sports and activities.
I feel that increasing the max skill rank progressively, even slowly, will eventually do harm to what E6 is trying to accomplish.
The Epic Defense Bonus progression that you've offerred troubles me, also. If a character were allowed to progress far enough, lower level characters would eventually not be a threat, anymore, just like standard DnD 3.5. This is something else that I feel works against the goals of E6. Ryan has stated that one of the benefits of E6 is that a Dungeon Master can build his/her campaign world like an amusement park because threat levels aren't all that varied between 1st and 6th level. Introducing an epic defense bonus ppoints to the possibility that there are some threats that are so far out of the league of 4th or 5th level characters that they don't have a chance against such a threat. To me, this poses a problem in E6 (though I'm sure others would disagree).
And, the increased Hit Points per bonus level? Why do it at all? In standard E6, a character could take toughness every 5K XP and gain extra hit points. To me, that's easier and simpler.
That's my take. The main question that I have for you is whether or not the house-rules you've suggested will allow you to
better play the style of game that you want to play.
Thanks for reading.
