Nope. They dropped the more unnecessary skills like acrobatics, and gave us perk trees. As for spell making, I like to think that it died out with the Mage's guild.
Acrobatics was only useless because there was no designs in the game that required you to jump further or higher to be able to reach a higher ledge, or get over a chasm that could help you escape an especially dangerous fight. Poor design choice, not the skill's fault. Lockpicking would be just as useless if the devs 'forgot' to put in locked doors and chests. The same can be said about speechcraft, another useless skill where using it gets you virtually nothing, and it certainly can't be put in the same category as, say, 'One Handed Weapons'. I kind of like the perk trees, but most of the choices are superficial. If you get One handed weapons as one of your favored skills, you basically choose if you want axes, blunt, or swords perks and then get everything from there on. Likewise, your rationalization for spellmaking is just that, a rationalization for a poor design choice. It gives a 'pass' where there should be an honest criticism. Why? Because magic kind of svcks. I virtually can not scale its damage at all without crazy robe enchantments, or buying new spells.
I can guarantee you this.
If you released Morrowind, Oblivion and Skyrim side by side in their original state upon release, Skyrim would hold up very well.
Without question it would. But you also need to consider the fact that Bethesda released Morrowind when it was a smaller, more obscure developer. They had dramatically expanded since then in terms of manpower and resources when they released Oblivion, and certainly once they released Skyrim. Also keep in mind the updated technology, and hardware available to the gaming community and its developers with the release of Oblivion and Skyrim. It's just not a fair comparison in the terms you've used. Also, many of the problems with Morrowind were things like bugs, or errors that could easily be corrected by patches or modders. Conversely, many of Skyrim's problems are fundamental - poor quest design, poor character design, level scaling, etc and these are problems that modders can't fix, and problems that would be virtually impossible and highly unprofitable for Bethesda to fix. So there you have it.
I do think that people who feel that Skyrim was a disappointment occasionally fall into the trap of saying that Skyrim is a 'bad' game. I feel this isn't true: Had it been The Elder Scrolls I: Skyrim, it would be beautiful to look at, have simple but interesting combat, and be notable for the scale and free-roaming nature of its world. You could also credit the wonderful writing of its books, and the fact that some have twenty pages or more, or mini-novels contained over several volumes.
However as Elder Scrolls V and a worthy successor to Morrowind and Daggerfall I think it falls short, and is a disappointment.