When I defeated Luminous I wandered around for ages trying to find out what I was supposed to do next. Resorted to Googling to find out I was supposed to go back to Eternity Port to end the game. :/
I think there should be an actual choice as to whether you accept Malina's offer to go to Eternity port rather than the only option being "[N]o, I'm going to continue exploring.", that way you can have a good satisfying and climactic ending, rather than one full of frustration and disappointment.
(I'm not sure if this post should be here or in the Commonwealth subforum)