I haven't finished the game yet, but based on what I've played I think Bioware should have really hit on the colonizer or conquerer angle a bit more and fleshed out the premise and backstory of the game a bit more.
Honestly, the Andromeda initiative? A bunch of nobodies who have "seen everything there is to see" in the milky way. Really?!
The foundation for the whole game should have been: while Cmdr Shepard was off doing his thing in ME2, a branch of Cerberus utilizes data he's gathered on the collector's stasis tech to kidnap settlers on a harsh fronteer world, load them into a bunch of retrofitted soon-to-be decommissioned Cerberus cruisers and fire them off toward the Andromeda Galaxy with all the prototypes and failed Cerberus tech that ultimately got piped to Shepard (SAM is a baby EDI, the tempest was the proof of concept for the SR2, etc).
This would have not only formed a solid basis for what the hell you're even doing in Andromeda, it would have explained why no one in the ME2 timeframe ever heard about the initiative and would have retroactively fleshed out ME2, which had the weakest story of the original trilogy (turns out the illusive man always hedges his bets, and if Shepard wasn't going to save mankind, manking would thrive elsewhere). It would also mean no milky way alien species, leaving more Dev time to actually make a varied set of interesting Andromeda species.
Most importantly, no one in Andromeda would have to answer the god forsaken filler question " so why did you come to andromeda?"
Your cruiser drops out of hyperspace, engines on the brink of total meltdown, you've picked up something (the scourge?) Out in darkspace and it's piggybacked on your ship ready to infect and spread. No less, you've just dropped into a cluster with a number of intelligent species, upsetting a delicate balance of power. And you were just a simple farm boy. The message is clear from the beginning: survive.
A DA2 story structure would have really been nice when establishing a basis for future stories in a new galaxy. The first act would involve finding a home/first contact/disagreements about what to do with the natives. Second act would involve uncovering the scourge problem, deepening distrust between natives and newcomers/ schizm within the milky way group over whether to conquer or coexist. Third act would be the big climax where you halt the spread of the scourge, settle the problem of hostile natives one way or another and ultimately facedown with a once ally now enemy who has split with you on whether to conquer or coexist.
Boom, instant tension, a sense of progress and an established world at the end the game.
The devs always said Star Trek was one of their guiding stars when making the ME games. I just wish we had gotten more Kirk/Picard/Sisko and less Wesley Crusher with Andromeda.