I looked at both as well. Nitro had faster processor, HD display, LTE, and the better likelihood of ICS (hadn't been announced for Atrix 2 at the time of my purchase).
But sadly, as others have said, Nitro felt laggy to me when I played with it in the store. SGS II Skyrocket felt much snappier though didn't want it cause lack of HD screen.
Plus Nitro was ~ $200 and Atrix 2 was free! In the end I choose Atrix 2 and haven't regretted it yet!
I haven't even done any modding to it - still in completely stock condition. Feels speedy; "4G" has been much better than my old Captivate for browsing, and although no HD screen, it is higher resolution than the typical Android - looks super crisp.
Plus battery life has been phenomenal! Both Skyrocket & Nitro have been blasted because of poor battery life. My Atrix 2 at the end of a 17-18 hour day is still at 60% plus.