If I'm not mistaken, hardly anyone (squadmates) questions what you do in ME3. Just Tali and Wrex. And if Tali disagrees, she kills herself. If Wrex disagrees, you shoot him.
So.
Shepard was made to have a squad of loyal minions, and I'm ok with that. Who wants to be surrounded by someone who constantly badgers and disagrees with you? (AKA Solas / Vivienne / Morrigan / Sera.)
Yes, I happen to be a Garrus lover, and yes, I see his flaws. But I thought I would point that out. 
In ME3, you can be in conflict with Kaidan & Ashley (Mars, Citadel Coup), Wrex and Mordin (sabotage Genophage), Legion & Tali (choose one over the other), Jacob (you can punch him if romanced) and Miranda (refuse giving her the Alliance resources, didn't say anything about Kai Leng, unloyal and she will die). Cause Javik to commit suicide and you can cause Steve's death if you choose to ignore him. And there's a bunch other characters who was simply killed off if they're unloyal (Grunt, Kasumi, Zaeed). Even Jack is even harder to survive unloyal through the suicide mission.
But Garrus stays the same. He was written to be a singular optional character without too much character development and stagnated as a passive character while surrounded by a bunch other dynamic characters. Killing Saleon, dealing Sidonis, those two don't even matter especially if he was never recruited in ME1 and survived SM unloyal. If you choose to ignore him most of the game, he still treats you like his best friend forever and talk to you like you're his bestie. At least with Liara, you can choose to be cold to her and not defend/baby her or anything and she will be more reserved but not out of character.
Having a character who is simply created to be completely likable, agreeable, blindly obedient and absolutely loyal without question is simply bad writing especially in Bioware games. Garrus deserved more than being Shepard's loyal pet. He deserved to be independent, to separate himself from Shepard's shadow, to be an adult and not be Shepard's cheerleader, to be successful on his own rather than try briefly and fail if he wasn't around Shepard or at the very least, are man enough to disagree or agree straight to Shepard's face.
I don't hate Garrus. I just don't romanticize him enough that I see him through rose-tinted glasses.