When I started reading it, I resolved not to compare it to Planescape. I didn't think that was fair. Planescape was its own distinct thing and Manual of the Planes never promised or presented itself as a continuation. It's just the planes. For D&D 3rd edition.
Needless to say, I frequently compared it to Planescape. Honestly, though, the comparison was not particularly unfavorable. The two settings are comparable in their weak points (an apparent failure to truly grok the nature of infinity, and alignment is kind of a drag), but with different strengths. Planescape was all about setting up a particular feel and making everything into one big contiguous setting and Manual of the Planes gives you a lot of options and things to tinker with. The best part of the book was the appendix, where it started talking about variant planes and cosmologies. It felt like something new, like a hint of d20's promise to be a lingua franca of fantasy roleplaying systems.
The appendix should have been the heart of the book, rather than an afterthought, but it was largely held back by the need to touch base with AD&D's canon.
Not that this was purely a fault, mind you. A lot of that canon is still pretty interesting. I think if this book was your first exposure to D&D's planes, you'd come away satisfied. However, there's also just a sort of arbitrariness to it all. Why is Acheron, the plane of eternal warfare, also a bunch of cubes floating in space? Why is the Abyss the only plane with infinite layers (and, really, why are "layers" still a thing)? Why the Beastlands? Because that's the way it was done in AD&D 1st edition, that's why.
But if you can get past the notion of a default setting (the prime material plane is officially Oerth from Greyhawk in this edition), there's still a lot of stuff you're going to want to use. The only parts that I would compare unfavorably to Planescape are the description of Sigil, which is just a sad shadow of a great setting, and the second layer of Arborea. In Planescape, it was called Ossa and it was largely shallow enough to wade through, making it a strange fantasy landscape with its own fey-like quality. In Manual of the Planes it's Aquallor (which is "the elvish name" that showed up in Planescape, but which I find to be terribly on the nose) and it appears to be a normal ocean. Maybe I'm just being picky because it was one of my favorite images from the setting, but so what if I am? It's a loss.
It also wouldn't be a 3e book if I didn't spare at least a little time to complain about the mechanics, but this is one of those situations where the errors are mostly pretty small. I don't love planar alignment traits or magic traits, but at least we're not getting the big table of fiddly modifiers we had in 2nd edition. Also, the prestige classes were pretty neat, but the spellcaster class is inexplicably better than the non-spellcaster classes, even when you don't factor in spellcasting. Why, for example, would a wizard-focused class get Plane Shift at-will when a rogue-focused class gets it only once per day, especially considering that the wizard can memorize and cast extra Plane Shift spells. It's almost like it's okay to give extra magic to the class that already has a lot of magic, because once you've got a lot of magic, adding more doesn't significantly increase your power level, but even a little bit of magic is going to dramatically increase a rogue's capabilities, so you have to keep it limited, in order to keep them feeling like rogues. Either that, or it's a way to balance out the Gatecrasher's unlimited-use +2 insight bonus to bluff, diplomacy, gather information, intimidate, and sense motive checks (no, you look up what sort of enchantment and divination spells a cleric or wizard gets at 9th level).
Finally, Orcus. Fuck that guy. The canonical ending to Dead Gods is that the events of that adventure had on effect on anything whatsoever. Which may seem to say that the Dead Gods adventure did not canonically take place and they're just retconning to new status quo, except "Orcus revitalized his wand, and with its strength initiated a spell of resurrection cast by one of his last faithful servants, the half-ogre Quah-Namog. Heroes from the Material Plane seemingly disrupted this ceremony at the eleventh hour, but Orcus returned all the same."
Who on Earth is out there thinking Orcus has even one-tenth the villainous charisma necessary to get away with this kind of bullshit? You could have just said that the canonical ending to Dead Gods is that no one bothered showing up. Why say that PC-analogues succeeded at the adventure and then the DM just went ahead and made the bad thing happen anyway?
But aside from that one thing, I don't think Manual of the Planes' flaws are much worthy of comment. They can mostly be attributed to being an early 3e book, made before 3e was well understood as a system and to being a relatively condensed book, which didn't have nearly the wordcount necessary to fully capture the multiple boxed-sets, supplements, and adventures that came before. It's actually my second-favorite 3.X book so far (behind Book of Nine Swords) and there are parts of it, like the alternate Prime Material worlds and new cosmologies, that I really love. Overall, a solid addition to the game.
Ukss Contribution: Dead gods floating in the Astral Plane. People build cities and fortresses on top of them. Metal as fuck.