Classes, classes, for the love of Pelor, CLASSES!
1.) Themes and backgrounds are optional (says so right on the sheet). If you make classes into themes, those classes only are playable with theme/background on.
2.) Optional classes lose customization. As a class, I could build a ranger to have the archer theme (and attack at a distance) or I could take the Guardian theme (and be a ranger-knight), but if I'm a fighter with the ranger theme, I am locked into only one type of ranger ever.
3.) Some classes signature abilities are too strong for themes. Can you make a druid theme which grants wildshape and poison immunity? How bout smite evil and lay on hands in a paladin theme? How bout death strike and shadow jump from an assassin theme? Remember that a theme is a collection of feats; is rage, wild shape, or bardic song equal to reaper, ambusher, or arcane dabbler?
I'd lots of classes defining what you do, with themes defining a focus or method of doing so.