Imo I don't think the ending is the only issue, I think the brain being the big bad all along just felt like it derailed things and took focus away from the dead three.
We barely even interacted with them either, Orin is probably the one with the most interactions and she's fun but not really that interesting.
Gartosh probably had the most potential but barely has anything going for him and there's no real political intrigue.
I just wish the game had focused on them instead, the elder brain is just not interesting it's kinda boring and generic and there's not much else you can do with it other than destroy or control it.
When you're dealing with people there's so much more you can do, but with the brain it just turned into space alien invasion reapers from mass effect 2.0.
