After a second read and some checking up of events from the comics referenced within I think I have more of an understanding of the going ons.
Still alot I don't like, but the multiverse stuff, and that G1 is now a singularity apart from the rest was an interesting twist that could only really have happened with the massive real time gap between 80 and 81. I actually like the ending more now that I figured out what I think happened, having 12 pods was a nice nod too.
It is a shame that most of the 21 issue run of Regeneration 1 could have been tossed aside or shrunken down to not fill the modern 5-6 issue arc for trade paperbacks and there could have been a better handling and pacing based more around this final issue. A good issue or two devoted just to tying up events on Earth, another for Nebulos and maybe some more time in the 80's issues for seeing what megatron actually did on Earth and to better resolve the rime/Megatron fight.
Looking For: Wreckers Saga TPB Collection (with Requiem)