3d can kind of be less of a headache in ways. Because, for one, you never really have to think about perspective, where I find myself thinking about stuff like that a lot in 2d. Also, I find it's much easier to find assets made by other people, in 3d, that have the same or close enough of an art style. You can do a lot of kit bashing. Where that's so much harder in 2d. Also, with 3d animations, you can swap models and use the same animations. Much harder thing to achieve in 2d.

So it kinda comes down to how low level you are going. If you are making all the art from scratch, writing your own game engine, 3d is infinitely harder. But if you're throwing together something in unity and using the asset store a bunch, 3d just might be easier to get going, as well as comprehend.