Personally, I think it would be good to go with the four, strong base classes (wizard, warrior, rogue, and cleric).
From there, I'd design things to use basically alternate class features. Perhaps name certain packages as predesigned classes.
Want a swashbuckler? Replace the fighter's shield and heavy armor class feature with Mobility Fighting to create a fighter that works in light armor. Perhaps, give up some of the heavy martial weapons for the Precise Strike ability.
Want a Saber Rake? Start with a Rogue, replace his augmented skill list with Mobility Fighting and replace Sneak Attack with Precise Strike. He'd be fairly similar to the Swashbuckler, but with some slightly different abilities (Evasion, for one). [This is an example of different ways of doing basically the same thing. Don't try and beat me over the head with how "inferior" the saber rake would be].
And so on and so forth to make Warlock, Driud, Ranger, Paladin, etc.
Also, you could leave the individual class "alternate abilities" available to those who want to construct their own special class - with DM's approval, of course. (There will always been different levels of tolerance for what constitutes "broken" - I say leave it up to DMs with some good advice on what should be generally acceptable and let them handle it for there. Short of sending game police, can't do much more than that.)
Creating a Bard and Monk might be a bit tricky this way, but it could be done - or simply make them a full class all themselves if need be.