I've had a few ideas that you might want to explore.
1) Themed Substitution levels. Substitution levels have been introduced in some WotC manuals (Planar HB, Races of Stone, Races of Destiny). It would be nice to get some substitution levels based around a theme like dragon, undead, nature, darkness, elemental, etc. that are appliable to any class (perhaps you could do it also for psionic classes and other classes presented in the 'Complete' series, such as warlocks, etc).
2) Racial Alternate Abilities & Paragon Racial Classes (such as those presented in Unearthed Arcana).
3) More abilities from the Dragon #304 article 'Prestige Races'. (ability to grow wings, to regenerate, to develop various racial & undead traits, etc)
4) Transformational Prestige Classes. Prestige classes similar to the Dragon Disciple (see DMG).
5) Monster Classes: Chromatic Dragons, Gem Dragons, Celestials, Devils, Demons. Please don't shy away from Epic Levels. I always wanted to play a Pit Fiend, a Balor or a Soalr from level 1 to whatever Epic level it goes.
If you need more ideas.. just ask. I have plenty more.