See the problem? The notion of level = HD = CR is an appealing one on the surface. But it only works if monsters are limited to the same sorts of abilities as PCs. Once you start adding wonky abilities, like the beholder's eye rays or the mind flayer's blast, you wind up in a position where you once again have a creature whose CR cannot equal its HD.
Mouse is right. HD=CR is great for creatures with few or no SLA or Su abilities, but once you start stacking those on, its CR is going to exceed its HD by quite a bit.
For example, part of the problem with Turn Undead (one of many, admittedly), was the ridiculous CR/HD ratio for the large skeletons and zombies. The Holy Word line of spells also became quite wonky, frequently hitting the BBEG (if of a caster persuasion) harder than his (melee) minions.
That's why turn undead should've been based on CR, not HD. The designers failed to realize that undead's HD are generally WAY higher than their CR (especially skeletons and zombies), and they were lazy - instead of looking at whether or not the system worked, they just ported the old one over, made it work with the new mechanics, and let it go at that. So we ended up with a system that requires you to look up your result on a chart, is totally different than the normal resolution mechanic (making a roll vs. a DC), and is horribly unbalanced.
Rogues can't make multiple attacks (3e)
Wizards can't cast more than one spell in a round (3e)
Spellcasters can't blast all day (Warlock)
Rogues can't sneak attack undead (Skullclan Hunter)
Constructs can't be PCs (Warforged)
PCs can't be permanently invisible (pixie)
Can't, can't, can't. You know what? If you accounted for it, I think you could build a PC that fired off ten offensive spells in a single round. Just because it hasn't been done doesn't mean it can't be.
If you had to design a game where the base classes are fighter, rogue, cleric, and beholder, you would find a way.
But would if be balanced? Would it be fun for the other players? I mean, come on - look at the above list, and tell us exactly how many of those are balanced.
It makes HD based mechanics (see Holy Word, 3ed Turn Undead) work. It makes monsters as characters doable. It makes polymorph and summoning easier.
While I agree that unifying mechanics are the way to go, the examples you use above DON'T work, precisely
because they're HD-based checks. This goes back to my argument that HD != CR (take note here, Klaus - this is another reason why it can't be done).
... Heck, the very existence of Pun-Pun indicates that 3E's strongly mechanistic philosophy isn't enough to stop loopholes popping up. So you might as well make explicit the DM's role as final arbiter, rather than assuming a super-intricate ruleset will make such problems disappear.
Finally! Thank you - I'm glad someone is willing to point out the DM's role as arbiter of "What's good in the campaign". The designers can't cover every single loophole - all they can do is design it the best they can, close the most obvious ones, make sure their mechanics work with the core and with any other systems they're including in that book (like if you're using PrC X from book Y), and ship it. If JoeBob the player find some loophole that he can exploit by combining PrC X from a WotC book and PrC Y from some third-party book, it's not the designer's fault - he couldn't possibly have foreseen it. OTOH, the designers DO let badly designed crap through; but it's still the DM's job as arbiter to say "Sure, this is okay," or "Oh HELL no."
That's why I would much rather see ECL or a modified HD that allows for 1 HD = 1 ECL regardless of type. since we already have HD that can vary, it's not that much of a stretch to say 1 animal HD = 3d6 for the purposes of ECL/CR calculation. Give me rules that work the same for everybody, and a set of rules that don't and I'm sure I can show you that it's a lot harder to accidentally create Pun-Puns in the first system, assuming reasonably intelligent design.
Why not just do LA like NWN does - it ignores racial HD (I, personally, assumed their were already factored into the LA calculation) and adds the LA to your character level. So, a mind flayer Sor 9 would be ECL 16 (though technically, it should be at least 17, since LA, IMO, should never be less than CR).
In other words, make it possible to add hit points (for instance) without adding a whole truckload of unrelated abilities. Which, actually, makes advancing monsters simpler, faster, and more elegant, which is what a lot of 4e is going for.
You can do that already - Toughness feats (which I hope they're going to make worthwhile, BTW...). Or, like Klaus said, just boost the Con score (which is a more elegant solution.