I'm inclined to agree. D20 Modern assumes that characters are going to multi-class, and probably into 3 or 4 difference classes. As such, there would be no great benefit to lump character classes together.
One idea might be to adapt the three-class model from UA - Warrior, Adept, and Rogue (I think?) - and then lump the 6-class model together: Warrior (Strong + Tough), Adept (Smart + Dedicated), Rogue (Fast + Charismatic).
Then, anyone who picks Warrior (for example) could choose from the Strong AND Tough talent trees, and (possibly) have a larger skill list to choose from.
One final thought - Throw in the Psionic classes of Battle Mind and Telepath, and combine the Wizard and Acolyte classes. Throw Battle Mind in with Warrior, Telepath with Rogue, and Magicians with the Adept. You're pretty close to making a "classless" system where one level allows you to branch out into different directions without having to qualify for and pick up new classes.
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That's BRILLIANT! Why didn't I think of this before?! *LOL*