If you are intending on selling your game, you should also be thinking along the lines of who your target audience will be, and what their PC specs will be.
But otherwise, 3D is actually easier at the end of the day. And with the likes of good engines like Ogre3D, there's no reason not to go 3D.
The pros and cons of RTS games are similar to that of any other games (expect FPS's of course). You have so much more freedom in 3D because you can actually use the "3D space" as if it were real, and it's all taken care of for you.
Say for example you want to add a particle effect to a weapon, in 2D you would have to put layers in and all that to make it look like the effect is wrapping around the weapon. In 3D, you just give it the necessary rotations and wala.