Surely a major difference--the major difference, for me--is that Daggerfall has no turn-based combat. That, combined with your being a party of one, can mean instant death. When playing DF, you are on edge every second you're in a dungeon, with your left hand on your (personally programmed) keys, ready to try to cast spell reflection, fight, or flee. The dungeons being incredibly enormous, this leads to a lot of wear and tear on the nervous system, but a great feeling of triumph when you completed a quest. I like MM 6-8 very much, but I do not recall ever jumping up from my chair (literally) when confronted with a monster, or simply from hearing the distinctive sound of a lich or vampire (before it materialized) in Arena, and that happened to me more than once in Tamriel (the Elder Scrolls world).

One habit I developed from DF is to "do" a dungeon on the first try. In DF, the entire dungeon respawns if you ever leave it--which is silly, in a way, but also forces players not to wimp out with portals and beacons, doing a little bit at a time and coming back with full powers. When you go into a DF dungeon, you are there to do the job completely, by yourself, on the first try. And this can take hours. (Of course you can try sleeping in the dungeon to recover, if you like taking risks).

I agree that the "pull lever X here and find you've opened a door a mile away" is very annoying, and DF is full of that. I recall some DF players saying they hardly ever went into dungeons at all. The open-endedness of the game made such play possible. (Some people never did the main quests, either. There was no real need to.)