True, but there's the counter argument that the most distinctive and possibly best feature of D&D is the spells. They're contained dumps of quantized rules exception. There's nothing about them that suggests they couldn't be a rules anchor for any rules exception you care to add.
One could also define feats as "quantized dump of rules exception" (pre-2e, there were a bunch of those dumps, to the point where that was the norm, though it's true that spells have always been one of them). So I think it's fair to compare spells and feats, and ask which is the more suitable base for a rules system.
Spells have substantial, but largely non-specific limitations on access. Class and level are obvious ones; you have to be a 9th level cleric to cast Raise Dead, but if you're a 9th level cleric you can cast pretty much any spell your class has access to of levels 0 through 5. Conversely, feats have fewer, but more specific access restrictions. Power Attack requires you to have 13+ Str, but a character of almost any race or class could conceivably meet that requirement. Feats also have iterative prerequisites, which leads to feat chains ending in more powerful and specialized feats, while spells do not have this structure. Many feats have no prerequisites.
D&D spells are defined by per-time use restrictions. You have to rest and get ready, and there's only so many you can cast in a day. They do not tap any centralized resource (i.e. casting a Fireball has no effect on your ability to cast Magic Missile), and there are no implications to expending these limited uses other than running out of spells (i.e. you don't become fatigued). Feats usually work constantly or whenever the player uses them, occasionally have circumstantial limitations, and very rarely have any per-time use limitations like spells.
Spells often create new rules (Confusion effectively creates the confused condition for example). Feats usually leverage existing rules more, granting modifiers to actions and circumstances described elsewhere.
Spells are more textually intensive and take up more space. Feats take only as much space as the concept demands. A lot of people complain about how much space is used the the 3e PHB for spells, let alone the 4e books for powers.
I know you won't agree, because you like more streamlined systems that build up from a simulationist core (as per your remark that magic could easily be a d20 based skill), but it's not like it's corner gossip on Insane Street in Crazy Town.
You're right. I don't agree. Not because I don't understand the approach, but because it does seem a little crazy when there's a simpler and more flexible "quantized rule exception" paradigm right there waiting to be utilized.
Having both feats and spells is really redundant (both 3e and 4e do; 4e just has a lot more spells, uses them for all classes, and less emphasis on feats). And yes, I do think it's best when designing a d20 game to adhere as closely to the core mechanic as possible, and for exceptions to be purposeful and worthwhile. I just think if you had to pick one approach between spells/powers and feats, feats are the way to go. Show me a system that converts the existing magic system to something based on d20 modifiers (skills) and feats, and I'm all for it.
If I was making a more cohesive 3.5, I would make the spell framework used for activated abilities (as it has the standard nomenclature for range, number of targets, save to use, etc.) and the feat framework for passive abilities.
I wouldn't. I think feats are a better framework for active abilities as well. Plenty of feats are actively used.