I don't think we should be having to compromise in our own heads for us to make sense of it. It's flat out stated that it's an alternate universe/timeline so I'm going to view it as such. That's not to say I didn't enjoy it, but knowing that the 'real' Kirk and Spock are knocking around somewhere else slightly diluted that enjoyment.
I didn't find it that complicated.
Of course I'm one of the few people who had no problem grasping the "vague sequel" nature of SR either, so maybe it's just me.

And in any case, the fact this is an alternate timeline doesn't make these characters feel any less "real" to me.