I'm another one in the camp of people who like Scott and Emma together, but hate Morrison's handling of them.
I don't know, it seems like, to me, at least on X-Men, Morrison was incapable of both having an idea that was smart, and executing it well. He could have totally stupid ideas (Cassandra Nova is Xavier's twin sister he killed in the womb) and execute them BRILLIANTLY, in ways that almost redeem the stupidity of the idea, and he can see things (like "Scott and Emma would make an interesting couple") and do it in a way that I hate, but once he's gone I can try and enjoy what's left by ignoring his actual work on it.
And for all his talk about how Jean was becoming more remote and godlike, it actually READ to me like they, as a couple, just got into a comfortable boring routine, combined with Scott having the equivalent of a crisis over the fact that his wife makes more money than him, and Emma being new and exciting and sexy.
I'd rather have done without the affair plot totally (it's one of my personal squicks, admittedly), but even despite that, I don't think it was executed well.