It's times like these that I really hate the dialogue wheel. There's very little room for subtle or even just deliberate roleplaying when you only have the vaguest idea what tone the character is going to speak in, and no idea at all what he's going to say until after you've picked your approach. But you work with what you have. I gotta say though, I played through the third game just last week and I can barely remember what the Geth "nonsensus" mission was even about, and I have no recollection of the scene on the Normandy you're talking about. How many times have you played these games?
Keeping mum about intending to eliminate its perceived species seems like a good idea if you want to exploit something, yeah. I'm mostly looking forward to getting into ME2 with this character. Love that game to death, and it's the one where you spend the least time actively fighting rogue AI, making anti-AI-ism in dialogue a little less... redundant.
I've played ME3 most often because the gameplay is by far the best of all 3 games which makes it more fun to play through. It is the worst one to roleplay though, that's for sure. When it comes to content, I like the first one most.
In the Geth "consensus" mission you have to enter a Geth server and disable it. The Legion/GethVI uses the opportunity to show you some vids from the morning war. Mostly propaganda that tries to show the geth in a better light, things like the 99,9% genocide on the Quarians remains unmentioned. For roleplaying it is useless since Shepard only has autodialogue here. It also doesn't really add much to the story as it is just some cheap sympathy grabber for the Geth that tries to cover up or reverse central elements of the lore, and the gameplay here is boring since all you do is shooting orange blocks. Probably the most useless mission I've ever played. The scene on the Normandy has been adressed by others, perhaps one thing
IIRC, there is no point when Shepard expresses willingness to kill the geth (the true geth, not Reaper-upgraded ones).
If I remember correctly, if you pick the renegade choice without asking Legion/GethVI if it is conflicted, Shepard says something like "We can deal with the geth easily after we destroyed the Reaper base". Different wording maybe, but very clear about Shepards intention to destroy the Geth, reaperized or not. You know, this is one of those situations where the neutral option really would make a lot of sense, but noooo...
Another "deal-breaker" for me would be talking to Ashley during the Rannoch arc. She has one of those Kasumi-like auto-lines, how she "rather snipe down a tin can than a person", and what she says then, suggests that Shepard kind of lessoned her for that or whatever. ("I'm right .... right? Fine I shut up", ugh ... cringeworthy). I don't know how it is with Kaidan.
Instead you could talk to Javik after the Dreadnought mission. When he asks why you brought a machine on board you have the opportunity to say that you are not happy about it but did not see any alternative.