I agree that constant bonuses are generally more "powerful" but are also often less "sexy". Sure, a +1/2/3 to hit is good, but you rarely hear somebody exclaim "Thank you Heavy Blade Expertise!" What's more, it doesn't do anything to distinguish your long-sword wielder from the next.
Some constant bonuses do though (such as weapon proficiency), but even they tend to become fairly standard (what avenger wouldn't want an executioner's axe or fullblade)? That being said though, while conditional bonuses are often more flavorful (my guy really likes to play with fire), they also run into the problem of being, well conditional. What wizard would take a feat that grants +1 to hit with a fire spell before taking the appropriate implement expertise feat? Where I think that certain feats can really shine though is in the area of class or racial feats. No longer are you just a dwarf, but you're a particularly fast dwarf, or a dwarf that is particularly protective of his friends.
Ultimately though, I think the problem really does come down to bloat as others have mentioned. The constant bonus feats are attractive not just because they are always up, but also because it often requires less thought in even building the character. I don't need to look through all the different feats, powers, and items to see how I can make the most use out of implement expertise as I might with something that gives a bonus to fire-based attacks.
I think the idea of trees and leaves is a really good one, that if done right could lead to a) easy to build characters and b) fairly distinctive characters. At level 1, you have say 15 feat choices. At level 2, you now have 16 (since two options opened up with your level 1 choice). fairly quickly, you'll be ignoring half the branches while still having the chance to make your character feel different from the every other character of your class.