The thing about LA/ECL is this: It never really worked.
Oh, you could play with it, don't get me wrong. And you could have fun with it. But the truth is, it implied a level of compatibility and equality that it didn't really deliver.
Mind flayers, for instance. Does anybody here really believe that a mind flayer is equivalent to a 15th-level character? Really? I don't. And my experience doesn't suggest that it is.
Is a thri-kreen rogue 2 really a 6th-level character? Not in my experience. He nearly died, frequently, because while he was hitting like a 6th-level character, he was absorbing damage and rolling saves like a 4th.
LA/ECL was a patch. It was a "Let's make this as close as we can." But it was never, ever truly accurate.
For a game to have monsters and PCs be truly equal, it has to do two things:
1) Limit monsters only to abilities that PCs have, with no exceptions.
2) Make monsters functionally identical to a PC of the same HD.
In a system like that, a troll is just a 5th-level fighter with green skin and no regeneration. I don't want that. It's boring. But the instant you bring regeneration into the equation, you've mucked up the system, because regeneration isn't exactly equal to anything PCs get.
Ultimately, I'd rather a system that gives designers and DMs complete freedom, rather than one that restricts them in order to almost accomplish the stated goal of monster/PC compatibility.