D&D is already designed that way. Endurance>Diehard. Combat Expertise>Whirlwind Attack. E6 has Ability Training>Ability Advancement.
As long as your prerequisite feats are tolerably functional (+2 to a save is nothing to sneeze at) I think it's okay. The primary concern is balance, making sure that players don't outpace one another.
It's fine if you write new E6 feats that have 6th level or 6/9 skill ranks or a base save bonus of +5 as prerequisites, as long as you cater to all of the character builds your party has. E6 already does this specific to each of the core classes, it's fine to write slightly more powerful feats intended for max-level characters.
One option the GM could implement is write feats that have specific quest or money prerequisites. Want to take a feat to get wings? Okay, you have to perform a quest for an elder air elemental, spend 4,000 gp of reagents and spell components, and perform a ritual on one of the 5 highest mountains in the world.
I'm actually in the process (the long, drawn out process) of making "epic" e6 feats.