Not only do I have no preference, but these sorts of questions are really the wrong thing to ask.
It's really like asking, "What's a better board game: Monopoly, or Mouse Trap?"
There's nothing inherently superior about playing in a three-dimensional space. What's important is that the game use the presentation approach to its advantage. That means that the gameplay, the mechanics, the story, the art style, should all be appropriately calibrated for the specifics.
Tactics in two dimensions is very intuitive. Turn-based tactical games like Final Fantasy Tactics Advance 1 and 2 in two dimensions (even when they include "height" it's really not much of a variable) make a lot of sense and lets you make interesting decisions.
In contrast, I find a lot of 3-D games to gain a little in comparison in terms of immersion but lose a ton immediately in terms of "mushiness" to the experience and a reduction in tactical depth. I don't think it's a coincidence that you listed Fallout 3 and Skyrim, two very easy games. The From Games series, Demon's Souls to Bloodborne, are obviously counter-examples, and those games made the 3-D motion a crucial part of their difficulty.