Splitting level-up benefits and allowing players to allocate benefits on a level-by-level basis would make for more organic progression, yes, but it's also a lot more prone to abuse. Feat prerequisites are a lot more pliable when you're not nailed to a static level-by-level progression (e.g. you can gun for a key +3 BAB feat right from the start, then ease back your BAB progression if you don't need it for anything else). Start-up benefits like weapon/armor proficiencies (and to a lesser extent saving throws, since good saves start with an extra +2) are also left as something of a loose thread; admittedly mixing progressive benefits with static ones is problematic to begin with, but if the progressive benefits are separated level by level it's even more of a headache.

You also have a lot more room for min/maxing. Most full spellcasters aren't going to have much use for BAB, so they'll happily dump it for a shot at more HP. Similarly if you're not a skillmonkey you probably don't urgently need more skill points, but bonus feats are awesome for everybody; if characters could buy them separately instead of having to take them as a package deal with Expert, many of them wouldn't think twice about selling their skills short for an even better bonus feat progression.

The end result? If you split up the tier benefits and let characters purchase them a la carte, you're going to end up with more powerful characters that are less well rounded. There's plenty of power up for grabs already, and I'm not a big fan of one-sided character builds. You could keep the power down by giving out fewer benefits overall, but that just axes versatility even further; as it stands the current tier system already struggles to match hybrid character classes (and that's even without looking at saves; it gets even worse if you do, since most hybrids have multiple good saves).

It would be an optimizer's dream, but that's something I'm trying to put less emphasis on. Don't get me wrong, there's nothing wrong with optimization; I just don't feel it should be as large a part of the game as it is.