I wouldn't say he's annoying seeing as he's pretty much right to be suspicious. Cerberus could have easily made Shepard their slave, Miranda very nearly did so, and they had clones to brainwash and send at them as well. Kaidan: 100% justified.
Yep, they wanted him to be a possible male LI in ME1 but scrapped it to avoid bad press, they still left what bits of data they had for it on the disk and someone made a mod for it on the PC. Which is also why they brought back the KaidanxMshep in ME3 and gave a nod to the mod.
Isnt it!? Of course, i'm a bit biased, since I have a PS3 and thus never played ME1... bt he was such a douche in ME2 when I met him. I mean, sriously Kaiden? I WAS FUCKING DEAD. They had to do less remodification on Robocop, you asshat. Then all he's done so far in ME3 in whine, no matter how nice i've forced my Shep to be. So, since he's such a whiny little bitch, he's been renamed ManBitch. He can go sit in the corner with Jacob while I play with all the cool team members -_-;