I hate the "3D" in many video games, in particular in strategy games. Beauty is appreciated everywhere, but for me the most important part is the gameplay loop/mechanics, however you call it. In a (real) strategy game that's decision making. You're reading the map of sorts, and come up with a strategy based on what you see. This 'parsing' of the map is a crucial element, and in particular an element I don't want to be challenging. That is, I'm not a fan of "find hidden objects" genre. I want the map to be very clear, with important elements easy to spot. Well, all elements involved in game mechanics easy to spot, as it should be me who decides which is important.
And here comes the problem with 3D: The more advanced a 3D engine, the more varying looks of the same object (e.g. metamerism): The object can be occluded (happens in 2D to a very limited degree), it can be lit at various angle by Sun (various angle if the Sun moves) and other light sources, it may have reflections, there may be a perpective distortion, and maybe some more.
All this means that a particular element can't be easily recognized, because there's no particular look that your mind may look for. It's just less readable. Imagine a strategy game, where you don't control your mouse cursor directly, but it's attached to a string to the real cursor, and swings all around as you try to click things. Interesting gameplay? Maybe, but not what I'm looking for when playing strategy games.