The narrative rhetoric between Illusive Man and Shepard is bad.

"Because you weren't listening. You're STILL not listening! Destroying the Reapers would be the biggest mistake we could ever make."

"Control the Reapers? You're indoctrinated! You're doing everything they want."

...Something was wrong with the way they wrote the ideological rift between Illusive Man and Shepard in 3. It felt like they wanted to "have" one, but didn't actually know what it was. All 3 or 4 encounters with TIM play out the exact same way. He immediately reveals he wants to Control the Reapers and doesn't say why, only that destroying them is a "mistake". Shepard says no, we have to destroy them, because they're bad obviously. Neither know how to do it, and they never actually talk about any plot-device that can do it, even though the ending reveals that yes, the Crucible does allow it, only for Shepard to make a nonchalant realization "So... Illusive Man was right after all."

Excuse me, auto-dialogue-Shepard, do you mean "right" as in morally correct? Or did you just mean "right" as in, Illusive Man wasn't crazy thinking it was possible? Cuz it's not very clear from anything that came out of the discussions we had, that you're now impressed or something.

The whole way through the game I feel like the arguments between the two can really be reduced to 2 old grannies going "Yes, I'm right" and the other going "No, you're not! I'm right!" but the thing that is supposed to make an ideological "Hero vs Villain" conflict interesting is completely missing. In a great story I'm usually like "damn this is some good dialogue" where you can't deny that the villain has a good point, but you just can't support it because he's clearly up to no good. But at no point in 3 do we actually have clarification of how we think destroying the Reapers is possible, even though everyone's like "The cruccciiblleee" and even though he probably wanted to do it using the Crucile, Illusive Man spent literally 90% of the game making incoherent Reaper experiments on his own, while occasionally trying to steal our data from us, only to discover that none of that was relevant, only actually using the Crucible is, and very briefly in the final confrontation can you hear Martin Sheen say "The Crucibles can control them, I know it can" (Hehe, he said it plural) but... that's literally it.

What's missing is clearly some sort of "No Shepard, there's something bigger at risk, even if you think the Reapers are the biggest problem. If we kill them we'll never be able to overcome X" or some other knowledge like "I've seen the records of all civilizations. Even with the Crucible, defeating that many is has never been achieved. We need ANOTHER WAY."

But it's never sold like that, he's just one-sided evil like "I'm so stupid, I'm going to go in everyone's way to do a science-experiment now because I'm the bad guy". and any of this criticism can just be discarded as "He's not himself, so give it a rest." Saren made sense, even though he was indoctrinated.

Turns out fighting some guy who can't form coherent thoughts isn't such a great villain, and even the final confrontation felt like you could remove it from the game, and the story wouldn't have been any different.