The problem with Skyrim and Fallout4 is that they're both simplified and marketed towards a more casual audience to such a degree that making interesting additions is very hard to do. In Skyrim you still have to deal with the limited amount of attack animations the game which prevents adding new kinds of weapons you also have to deal with the completely gutted magic system and the lack of skills.
I think the "lack of skills" is not really a hindrance to good mods. How do more skills help with modding interesting content or mechanics? To me it seems they just cut out a lot of superficial skills that were basically just padding. I do kind of miss Medium Armor and Acrobatics, but that's it. The rest of the skills that were gutted are filler.
Regarding animations: Don't know, don't care. The same goes for new kinds of weapons. Having mods for weapons seems kind of… boring. See later.
Yes, many mods make out of Skyrim something that it should have been all along. I don't see the problem with that – in the end I get an awesome game, and one that shows much more potential than Morrowind does, mechanically speaking. Something like Frostfall, Immersive Patrols or Civil War Overhaul simply wouldn't be possible in Morrowind, as far as I can tell. Even worse, the interface itself restricts modding severely.
The problem lies, of course, in the storytelling and the relatively usual landscapes and architecture. Morrowind's biggest boon for me is how utterly alien it is and that is missing in Skyrim, although not as much as in Oblivion, so that's good.
The loss of magic engineering is kind of sad, yes. I think they abandoned it because it isn't that interesting the way it was in Morrowind and making it interesting is kind of… hard. Actually, the alchemy system suffers from the same problem. Simply matching up strings doesn't seem like alchemy at all. Experimentation is absolutely straightforward, and that problem is not new in Skyrim.
The enchanting system in Skyrim makes more sense to me. Having to destroy some magic weapon to then realize that the weapon you are going to create yourself is going to be inferior… That's hardly "dumbing down".
In short: Morrowind's mechanics are full of cruft and they have cut down on that. Cutting away complexity that doesn't really add meaningful choices to the game is a good thing when you're making a game, and when making a simulation additional complexity only helps when the rules are actually interacting with each other. That isn't the case in Morrowind – or how does having "Short Blades" and "Long Blades" interact with anything else in any meaningful way at all? That I can use less weapons on a given playthrough? Doesn't seem worth the hassle, as the choice of which weapon to use is as boring in Morrowind as it is in Skyrim or Oblivion. You look at the stats and that's it. Reducing the number or weapon skills only mean you now have to decide between two skills in the beginning instead of choosing between however many there were in Morrowind.
On the flipside; Skyrim, though I thoroughly enjoyed it enough to put well over a hundred hours in it, had a problem where it felt like every character was expecting you to succeed and be special. They were generally unique and colorful, but they felt like they put too much importance on you. In Morrowind it felt like it was you against the world, struggling to prove yourself and make more allies as you worked your way towards becoming important. Power was achieved through hard work and adversity. Not that it necessarily wasn't in Skyrim, but it felt more like you were just being pulled along for the ride and propped up with power. It wasn't really a difference in structure, but it was a fundamental difference in presentation.
Also Skyrim refuses to slow down. Morrowind flat out tells you to go out adventuring and to slowly work your way through the main quest, and it has several parts where the main quest is thrown on the backburner as you're thrown into a non-linear sequence of objectives to complete before it'll pick back up. Skyrim's main quest is a linear sequence of events where the characters are constantly racing from one location to another and then they seemingly just wait around on their asses for you to show up but act like you had come straight there with them when you do. It all plays out like it should have taken a few days at most. Fallout 3 does the same thing and it irritates me as well, especially since the main quest there covers like 1/3rd of the map.
Yeah, that is definitely true. Being treated as special is really annoying and having other people talk about time but practically ignore it is really damn immersion breaking.