ME2 was filled with a lot of inconsistencies that at times I just ignore its flaws (particularly with the DLCs). I know everyone love the game but boy it was riddled with a lot of plot-holes... and whenever I get this feeling, I write fanfiction and fill in with headcanons.
Since Normandy was destroyed a month after the final scene in ME1, I headcanoned that it happens several months after Saren was defeated. This answers to why the Presidium were cleared up and look pretty and during this period, Shepard and Kaidan continued their relationship in secret. As officers, I don't think anyone have a problem with them having a relationship but it was problematic since they're both still attached to the Normandy. One of them still need to leave before they got into more trouble. I think Kaidan was prepared to do so and obviously they had plans for their future before they were ripped apart by heartless writers who don't give a crap about them.
In ME2, I reasoned enough that Kaidan's absence didn't bother me much, he need to be in the story to make his presence felt. During the Normandy destruction scene, we get to see the last time Kaidan made a decision to abandon her to save the rest of the crew and that was the last time he saw her alive. We don't actually know what happened in the two years while he was mourning except that he became Anderson's right-hand man, I think he part-time as an instructor and he was already running spec ops with his biotic teams before they made it official and gave him a proper division. And Joker hate him. That last bit was mind-boggling until I realized that Joker had a crush on Shepard and everything made perfect sense.
And then the interesting bits with The Illusive Man/Shepard/Kaidan dynamic. TIM did constantly threatened Kaidan's life to control and manipulate Shepard. Imagine if Shepard was too late and Kaidan was taken, he could have died at the Collector Ship and then she could have watch him die at the Collector Base. I wouldn't hold it against her to want to stay away from Kaidan to keep him safe and I think he realize that much later. That's why he pursued her rather than she pursuing him back.
I wished there's an alternate scene where TIM would threaten to kill Joker and Chakwas if Shepard refused to work with them. But I guess it would ruin the "Cerberus is harmless" vibe he was trying to sell.
Headcannon really does fix everything
because if we don't the plot has so many holes and jarring inconsistencies 
though keeping their relationship a secret is probably the best route since regulations and fraternization is frowned upon by the alliance tho it all goes to hell in ME3 when everyone starts too hook up but we'll end of the world and all that xD though I kinda want to know how you think joker coukdnhave a crush on shep? I see the hints but I'd like to know your details about it 
annnd the thing in horizon did scare me a bit cuz I was worried they'd go down that route with kaidan caught and turned to some liquified version of himself >.< gawd... Thankfully though he managed to escape I'm going with biotics and luck... Though I love how he is more confident in ME3 and starts to well pursue her first I actually see tkm subtly threatening shep if she still refuses to help them after horizon but I also can see shep being so duty bound that she can see there's a real threat going on so she has to push on no matter what
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