I honestly did not notice any of the deviations from the Prime continuity. The characters of Pike, Boyce, Number One, and Spock were written well and felt like the same people from "The Cage" a little earlier in their careers.
I definitely agree. The only two things I noticed that differed from 'The Cage' were (as others have noted) the presence of Colt as Pike's Yeoman and the usage of phasers instead of lasers as weaponry. The former didn't bother me, as I figured Colt might have been a secondary yeoman or something, who moved up to full-time service after the Rigel VII incident, and as for the latter, I just assumed it was a technological ret-conning on the basis of what we now know about what lasers can do.
My favorite small character bit, which I'd actually like to see followed up on in any future Dave Stern-penned Pike-era novels, is the comment from the female captain (sorry, I've forgotten her name), "Don't talk to me about Robert April." I laughed out loud at that.