Here's why I don't like this:
Imagine a scenario in which a DM is creating custom Themes for his campaign. Per your preference, he's creating a "topper" ability for each Theme. Now imagine that one of his players come to him with a concept for a new Theme. Does he get a topper ability or not? What if his Theme idea is *based* around the topper? Suddenly you've got this whole other type of ability that you need to consider in character creation, and you haven't solved the original problem.
Custom Theme in my post just means picking feats instead of a published Theme. Well-chosen feats are likely to overpower whatever combinations WotC chooses for their published Themes, if the Theme is just a package of feats.
If the DM wants to houserule new Themes in the vein of the published ones, that's very different. Naturally, as with all houserules, he'd have to use his judgement. If the combination of feats seems sub-optimal, providing some additional bonuses may be prudent.