CRPGs offer little to no freedom, and offer no flexibility beyond what has been anticipated, by design. That's not a flaw, just a design factor. You won't be playing a Mystic Theurge or using a house-rule in BGII, no matter what you do. And the difference between choosing a text reaction in NWN, BG2 or KOTOR and actually portraying a character in your game is fairly significant.
Most of the items on Ragnar's list are not dependent on level, and mega-modules don't necessarily have to have anything to do with level, either. RttToEE starts fairly low, and disappears at medium level. Banewarrens even moreso. I view mega-modules as a customizable tool that I can retrofit...and it's a lot less work for me, as the DM, to adapt the Crater Ridge Mines to my version of Greyhawk or FR than it is to create all the maps, stats and so forth. RttToEE's big weakness (to some, such as myself) is that it has a long dungeon-crawl as it's center-piece....the Hommlet portion of the mega-module is outstanding, and if the town near the CRRM was as fleshed out with NPC plots (or if Hommlett were closer), I would have no complaints.
Some players really enjoy going into a dungeon, killing the monsters and taking their loot. Diablo is just a distillation of this to it's purest form. And taken to a certain level of simplication, most modules or games fit that mold.
Case in point: examine Bastion of Broken Souls. It matches much of your high-level criterion. It features a world-saving plot (children being born without souls), interplanar travel, you need to defeat an ancient dragon (Ashardalon), uncover a plot, are betrayed by a powerful NPC, possibly make powerful allies of some celestials, lillends, druids, the dreamer or a fallen god, face poweful infernals and so forth. But, here's the thing: I can do that at 5th level in Hommlett in RttoEE, too. Do, in fact, when you fight the Blue Dragon, befriend several powerful NPCs, are betrayed by several others, travel to a demi-plane or two, uncover several plots and so on.
I used Bastion of Broken souls for a short while, but it was unsatisfying, as any module that I hadn't modified would be. Scratching the serial numbers off of a dungeon and calling it a demiplane or something else doesn't change the reality that you're still going somewhere and killing something and taking it's stuff. My players much rather enjoyed the module I created myself, instead, which was more relevant to the campaign. In it, they travelled first to the Elemental Plane of Fire; travelled to the City of Brass, met with an old friend, a Djinni Prince, at his court; were tracked by some mysterious enemies, and uncovered a plot back on the Prime; travelled to the a gate leading to a demiplane and defeating the half-fire elemental Paragon Beholder guarding it, and then leading a lightning raid on one of the fortresses to release their captured patron, an Ancient Gold Wyrm. One of the best adventures I've ever run....and impossible to write for a larger audience, as the campaign is so specific to the characters and the setting.
I'd love more varied mega-modules, too....but I don't think the format is invalid, by any means.