The emperor is written like an entry from wikipedia; illithids have always viewed themselves as superior and everyone else as lesser, and that is what the emperor meant by evolution. Even him dealing woth loneliness by mind thralling Stelmane is classic mind flayer. The only unusual aspect of his personality is that he remembers being Balduran, before BG3 this was only possible with gnomes. The only mind flayer that is the outlier, is Omeluum, as he indeed does not act as expected.
The issue is that even if the manipulation is obvious, due to the above, you still have go along with it. Because the interactions with the emperor, even antagonistic, don't matter. With Daisy there was an alternative path at least. Effectively the emperor is just Larian making it easier for thrmselves, because instead of writing two paths through the game, there is just this one with no reactivity.
Couple points. Omeluum isn't an outlier in this particular sense. Mindflayers that have or are born with arcane power exist in the lore and they usually go one of two directions: killed outright or they escape/get kicked out because the arcane power makes them especially resilient to control.
The Emperor on the other hand is just a normal ceramorphosis'd mindflayer, and as he tells you himself he has no such ability to resist an Elder Brain. The memory you can kinda get away with handwaving since he gets rescued quickly after the infection. Spending enough time with those memories and without being controlled would probably make that sense of self stick more as Mind Flayers used to develop independent personalities before the Elder Brains took complete control of their colonies as a survival measure after their empire was overthrown. The main problem with the Emperor isn't that he remembers who he was, it's more that in spite of EVERYTHING he says and does, if the toddler doesn't get his way he just takes his ball and goes home. That only makes sense in the case where his goal was always to rejoin the colony which it explicitly is not even when he leaves to do it.
There's also the issue with who the Emperor was actually supposed to be. As far as I can tell, he was retrofitted into the role of Guardian, and Daisy was going to have a different far more thematic approach while he was going to have something separate going on at some point.
