Hey Pfhoenix - I really like the idea of what your doing here! Words of encouragement! Words of encouragement!
I noticed an issue with choosing Class - Say you start and choose a class like Cleric, Save the character, then re-load that character. Say you think about changing class, so you choose Fighter. Cool, that works. SO you decide to change back to Cleric.
It looks like it doesn't clear out the old Clerical "Class Features" or "Encounter Powers" (that you get for the class) - but instead adds a second set.
Suppose you then switch back to Fighter - some of the Cleric Features and Encounter powers are still there, in addition to the Fighter Features and Fighter Encounter Powers.
And if you then switch to a different class (say Ranger) - it looks like its still hanging onto that one extra set of Cleric Features and Encounter powers.
Its of course easy enough to just click the little "-" and remove the excess - but I thought you might wanna know.
RE: the Racial ability score Mods - [and this is MY opinion only] - I also found that to be not to my liking. I understand your thinking about not changing the user's input and trying to stay as close to the "official" char sheet as possible... But I just can't help but be thrown when I look and DON'T see the real total for my Eladrin' Dex and Int scores. Even though the ability mod is for the modified stat, and it looks like all calculated places use the modified stat... dangit, I'd really prefer seeing the final, modified total stat there. I'd be fine with having the extra "Base Values" column.
Like I said - just my opinion. Feel free to stick to your original plan!