Most bosses are pushovers in the Inverted Castle, but you can't deny that the pure novelty it brings to traversing the castle is at all a bad thing. The same goes for the truly open-ended progression it provides. Now you have all the powers, and the whole castle is waiting to be explored, and now you choose where to begin and end this exploration. The inverted design actually is very clever (probably accidentally, like thernz said), because it allows you make extensive use of previously almost unused powers (such as the super jump and bat form), not to mention that there are new, deadlier enemies (I'm probably the only one who thinks that the Inverted Castle, minus most bosses, is an actual challenge), all of which significantly change previous areas so they might as well be new. The only remaining things are the layouts, and the tiles, which have had various colour filters applied which is quite effective at changing the atmosphere (with help from the new music, of course).
The lack of tracks is the only real problem I can think of in the Inverted Castle. I don't mind less plot, because we already know all that we should by that point, and plot isn't all that important anyway. Besides, the last scenes with Alucard and Dracula are great enough to make up for any lack of plot.
It shouldn't be comparable to Portrait of Ruin, which had horrendous level design to begin with, and just regurgitated that level design to make four new (somewhat altered) stages. The werewolf wasn't bad, but otherwise, the stages really had no redeeming value, unlike Symphony's Inverted Castle. I don't particularly like Ecclesia's reusing of some stages, either, but at least it did good with them by having significantly different layout and enemies/enemy placement (the swamp was basically Ruvas Forest, but it had those segments that slowed you down and the hills, besides the different enemies; they at least tried to make it different enough so that it isn't a total retread).
Zero nostalgia in this post, by the way.