Sure... that also means the powergamers out there CAN sift through all the boring flat bonus feats and attempt to build their own 'super-themes' that supposedly make them Uber-Fighters... but if the designers have done their job... EVEN THAT won't really make the character all that more powerful that the regular Boring Fighter Option themed character.
It's that last bit that's the problem. WotC has not, historically, done a very good job of forestalling the powergamers--though I admit they did a better job in 4E.
I'm not a big fan of themes being conglomerations of feats, but if we're going to have such themes, I think the solution here would be to have the feats from Boring Themes be mutually incompatible, perhaps based on class*. Thus, there is no option to cherry-pick. You can take the whole Boring Theme for your class, or half the Boring Theme and half real feats, or all real feats, but you can't pluck the best features from each Boring Theme and stack them on top of each other.
[size=-2]*And no sneaking around this restriction with multiclassing, either.[/size]