2D really simplifies everything, but not to the point of transforming it entirely -- in short, working in 2D is a great playground for learning to work in 3D later. Take physics, for example, 2D basically means you have only 3 degrees of freedom (translation along x, along y, and rotation in the X-Y plane) to deal with, rather than 6 (X, Y, Z, Roll, Pitch, Yaw) -- everything is basically the same, its just less of it and the simplifying assumptions you can make.
You probably are better off starting with 2D to get your bearings if you're new. One of the most difficult parts of making your first complex game is figuring out how all the parts fit together and interact -- and its almost entirely the same whether 2D or 3D, but you won't have the 3D details holding you up if you start with 2D.
But I guess that really only goes if you want to write those systems yourself. If you're going to use Unreal Engine or Unity or other engines/middleware, you'd probably be fine to choose either if you're very confident that your math skills and reasoning skills are up to the task. Just keep in mind that basically everything is twice as difficult or more in 3D than in 2D.