Xini, here's some honest advice.
What you want out of a game sounds interesting, but it is not even close to core D&D 3.5. At this point, you have three options:
1. Pursue another system. Some other posters have described some good systems here.
2. Use variant rules that have already been published. The Unearthed Arcana has a lot of great ideas on this, many of which actually do address your concerns. If you haven't yet, I'd highly recommend looking at this book.
3. House-rule the heck out of the system. This would be a lot of work, but you may be more comfortable with this as it provides the greatest degree of customization.
Personally, I'd look at option 2 first, and proceed to option 1 if I didn't like what I saw.
For what it's worth, an "error" implies that something was done incorrectly, which means that there must be something correct to compare it against. There isn't. Game preference is a matter of personal opinion, not empirical truth. Stating that the design of D20 is in error is flat out false. Without question, the design has created what some people view as problems, and this is a good place to discuss those.
As for why some people labeled you as a troll, comments like these don't help:
Xini said:
I do hope that any version 4 that the mages of muhlah come up with is an improvement but I fear that they believe so strongly in the d20 religion and the infallibility of the original D&D concepts that we are liable to be left with a simple rehash of what exists now, including all the flaws.
They're inflammatory and denigrating.