That's fair enough. I remember playing CSS back in the day and just shaking my head profusely when my friends invited me over for Halo 2 LANs. Needless to say, after playing both for a long time, concurrently, my outlook has changed. I understand the limitations of a controller but the feeling I get when playing both at a high level is the same.
In both there's a direct correlation to how much time I put in versus how consistently I'm able to perform successfully, that to me is skill. In fact Halo is almost designed with the controller's fallibilities in mind:
Instead of demanding a reflexive, accurate shot like CS, it decides the superior player by how long they're able to hit a fast moving opponent over an extended period of time (with higher health). This way there's still a dividing line between the poor and the good players that involves aiming, just in a different formation to that which suits the mouse.