I've been working alot with making characters for D20 for a big 11+ person game I"m going to run.
All the players are playing themselves (sort of a running theme with me) and alot of them are Smart heroes.
And they're absolutely nothing alike. I find that having 6 people take the same class and have almost no overlap in skills and feats is pretty sweet.
Then I have a Tough hero who put alot of skill points into traditionally Smart skills because of Class-Skills opened up via Starting Occupation.
All-in-all, getting in and working with it, I haven't found the class system of D20 Modern to be restrictive. Just the opposite. Hundreds of perfectly viable combinations are there, and the system pretty much does the work for you.
I've played Classless systems before. Everybody vaunts the customizability and how you can find the "Real" hero you want to play. *shrugs* It's just harder to balance, in my opinion. It should all be balances and trade-offs. The Basic Classes system of D20M, as one poster said, basically just does all the troublesome balancing for you.
Because if you DON'T balance correctly, people will abuse the hell out of your system. "Customization" and "truth to the character" aside, super-complex point-buy systems have, in my experience, always degenerated into an excuse to min-max a super character by abusing the little loopholes that appear all over.
Your Mileage May Vary, of course, but I'd suggest sitting down and playing a few dry runs with the classes as they are now and seeing what you can and can't do. I've run into ONE problem ... two people have taken a few years of martial arts and they feel they should get Combat Martial Arts. It's a Feat problem totally unrelated to the classes but for the BAB issue. You have to have a BAB of +1 to take CMA, and the only basic class that has +1BAB at 1st level is Strong.
*shrug* Other than that, not a complaint or a problem. I convinced them to take Defensive Martial Arts instead and I think everybody is happy.
--fje