My first thought of reading this blog post is, "Huh...I really should
rerun finish Age of Worms!" I got my 3rd Edition group up to Shadows of the Spire (I think that is what ti is called), and it just feels like a darned shame to just leave them stranded in the jungle. The horrible, worm-infested jungle... Maybe after I wrap up A Sundered World I can get them to go back and try 3rd Edition, if for no other reason than to houserule it up and see what we like/hate about it.
Feats are basically a game currency that you can spend to increase increase your numbers (ie, Weapon Focus or Toughness), add additional things to something (that warlord feat that lets you add your Charisma modifier to you inspiring word, and another I think lets allies make a save, too), or give you an entirely new thing to do, or eat least another way of doing something else (that eladrin feat that lets you fey step to dodge something).
My question is that if each class is supported by different pillar ratios, then why would each feat need to be applicable to all of them? Presumably if I play the game without feats it will work out just fine (if a bit harder), so why not continue making feats that cater to different pillars? Lets say that a player starts out with a fighter with the slayer theme. She is all about combat, but a few sessions in discovers that the game is more exploration- or "roleplaying"-oriented. Given that the math is purported to also be flattened, why can she simply not grab a level in an "exploration" type class (ranger, rogue, druid, etc) and/or retrain a feat?
Additionally it is not like feats have to be limited to one-or-all pillars; you could have feats that provide a benefit to one, all three, or just two on a case-by-case basis. This avoids the designers having to uniformly shoehorn a set number of benefits into a feat. Players who want something complex can take a feat that gives them an entirely new thing to do (like a skill power), while players that want to keep things simple can just nab a "+2 to two things" feat.
I guess that makes my answer "something else"; have feats do what you want, or even need, them to do. You do not need to set restrictions on them. I do not know how feats will differentiate themselves from class features (especially given that in some instances they sound very much like class features), but I liked what they did in past editions. I just think there should be less of them, and that the designers should think very carefully before giving us stuff like 3rd Edition's Toughness (one-time hit point bonus of three) or Cometary Collision (ready an action to charge a monster that also charges).