Yeah, all those things are fair points. Ending is a mess narratively speaking, but it's as such probably because last, fast changes and cutting of content done just before release. That being said it should be revised so the flow of narration and world-logic is maintained and consistent. The outcome should be defined by our choices and the characters we've met during the adventure should be more accounted for in the end. Right now it's connection to both of those things is severely lacking, not to mention coherency of NPC's behaviour in that particular ending scene. Creator of a narration should always have in mind that reader/player don't have the same thinking logic and we'll not understand what characters have in mind unless it will be, well, thrown in our face one way or another. I think this is one of the problems with the later part of story, it was done fast and didn't take into account that players can't read between the lines because they can't see them and can't see the greater whole.

Well, I already said some things on the topic of Emperor and Omeluum in another thread, so I will just copy them here:
[...] I personally don't understand why we're so railroaded with some of the characters. Like... the Emperor and Astarion(at the beggining of the game) are mirrors to each other, survivors!(and mind you there are other situations like that in game...) If you understood Astarion's character and gave him a chance and the Emperor cleary saw this... if You've met Omeluum and was friendly with him, and yet again the Emperor must have know about this... Why would he not give you at least a chance to explain yourself, appeal to his reasoning? Especially if You somewhat bonded with him! Why not promise You that he will let Orpheus go after all of this(and indeed make him the evil one if he would eat the prince behind Your back, that would at least give us a real and serious reason for wanting to kill him and a cool plot twist for scheming character)? I see him going to the Netherbrain as a desperate attempt to preserve himself, but only when all other choices would have been outed and how is it handled now shows he doesn't even believe in Tav's and companions abilities to preserve themselves which contradicts precisely all of his mighty plan to build up trust with them and use them for it. Why using things that You know wouldn't work? frown

And Omeluum... I greatly dissapprove how he was used in the story. Cleary his only purpose was for us to see that there can be somewhat good aligned mindflayer and to give us some boon(which have a lot worse meaning storywise and mechanicaly in full realese of the game). That just it. Meeting him don't have any meaning for the Tav and companions, they don't even have a serious talk about this; there is not even "oh, the Emperor is mindflayer, we know another one we could ask for advice in this matter" talk. The narration unreasonably takes from player a choice for Omeluum to be an ally in the end of game in which one of most vital points is freedom from Elder Brain for a mindflayer! You give player a character that have a power to get himself out of control of Elder Brain, capable of self sacrifice and think nobody would think about asking him for help in the matter when he cleary also is in danger along with all the Sword Coast if the Netherbrain plan comes to life? It's a huge overlook in various ways for me.