The beginning of season 4 had no real plot. You can't end a multi-year run of a series that really hasn't had stand alone episodes in favor of stand alone useless episodes with new characters that frankly suck.
I watched the special feature talking about production of the miniseries and they seemed to hint at that Pilot's set wasn't destroyed, that they loved him after all these years and he's still great. Maybe they stuck it together wrong. I didn't notice any big chances, maybe they needed to make it smaller?
Scorpius was a brighter white, but nothing too bad.
Ben Browder lost a few crystals on the bottom of the ocean.
I'm just glad we got what we got. But I can't help but to think of what a 6th or 7th season would have dealt with. The war most likely would have been season 5, maybe a little into 6, but then if John loses all his wormholes no more going to Earth, no more much of anything. It would have been great to see what new threats they would have come up with.
Now I need to get the comic books, there seem to be a lot of them.