Oh, how I'd wish for any sort of thing following up Macross II!
Heck, for an RPG, I imagined the idea that the Marduk were Protoculture or perhaps Zentraedi dissidants who watched the original Republic fall apart becuase it kept trying to assimilate cultures and blend them to ascend to greatness. (Thus the whole adoration of the Varja, the fan-idea that the Protoculture had known of the Galactic Whales, and their inpiration upon other worlds...)
The Marduk consider this to be what led to the Protoculture's destruction and thus goes out of its way to wipe out other cultures before it could contaminate and threaten them. I would imagine that would include Earth's colonies.
Funny thing is... then you could imagine the Alus to be a ship of the Marduk that breaks off from this plan and sets off to try and discover what happened to the race they abandoned.... (But of course, if memory serves me correctly... DYRL tries to say the ship was a part of the Supervisionary Army, right?)
(But you know, the VF-2SS does have some rather interesting design similarities to the 25 and the 27... a transformable armor pack, a heavy beam cannon... man... some clever rewriting and... heh...)