Sure they had the struggle with Earth, but that seemed almost beside the point to the fact that everything in the Pegasus galaxy went their way without any struggle at all.

Yes, exactly! I really think this diminishes it.

And I can see Sheppard leaving Earth behind, but I doubt even he would do it without a second thought - mostly because he would be aware of all the problems this story neglects. After having lived through season 1 and all the problems they had due to their isolation, he wouldn't make that kind of choice lightly! But not only did the story take away all the problems, it also took away any previous awareness of them.