BeastProwl wrote:What I find strange is that Megatron doesn't recognise the ship as Trypticon (Or so it would seem he doesn't)
I've always understood the continuity between the War for Cybertron games, the Exodus/Exile novels, and Prime to be rather loose. It wouldn't be surprising that Megatron wouldn't recognize his ship as being Trypticon, just to keep people who haven't read the books and/or played the games from being confused.
Another alternative: the current Nemesis isn't Trypticon at all. It's been a few millennia/eons since the Cybertronians left their home, after all. It wouldn't be surprising that Trypticon's been lost/elsewhere in the universe after all these years and Nemesis is a completely different ship. Especially since both the Harbinger and the Nemesis seem to share the same design (hard to tell since the Harbinger is in peices).
One thing the episode didn't explain was why the ship, under Dark Energon influence, was going after ancient Cybertronian relics. Ratchet does ask, but the ship basically hangs up on him. Hopefully, it doesn't go unexplained.