At a very minimum Samus needs her relationship with metroid itself changed. Because of the title itself, she always needs to go after the metroids. Just like aliens :p.
That is limiting the series in a big way. It's always investigating this of that facility.
Maybe the metroid should be some pet-like, last of its kind creature she has on her ship, who powers her suit and the space pirates would be her main enemies.
Then she can track any story or bounty in her expanding universe without that limitation. You can then almost send her anywhere.
In the wilderness we go alone with our new knowledge and strength.