Yeah, it's sad as it limits RP. My last Shep didn't trust aliens but got over it by ME2. Now I'm playing a super super racist Shep and all I can think to do is to give him a wake up call at the end of ME2. Seeing how ppl say you can't be racist in ME3 I was thinking of Shep ignoring and hating the aliens in ME2 all the way through, even ignoring their upgrades as he doesn't trust them. But then that will lead to
In the six month gap between games Shep will realise he was reason that that happened, and feel super guilty as he was close to that person. That'll make him reluctantly work with the aliens in ME3 even tho he still doesn't like them, as he knows he needs to for the sake of humanity.
Meh....that's all I've got. But if I could continue to be a racist humanity first jerk, I'd have gone with that instead. 
Maybe it makes sense. Maybe after all they've been through in the first 2 games Shep would have to start giving aliens their due. Maybe it would be daft to continue to feel superior to them. Or maybe Bioware just wanted us to be nice guys this time. Who knows *shrug*
I hear you
My first FemShep I played was a colonist and she didn't trust aliens. That was a lot of fun in ME1, and to an extent in ME2, but it's hard to be anti-alien for long, because even if I was mean to them in ME1, they gave really likable answers to that, haha.
I like your approach for ME2, sounds great.
By ME3, they took away this option, but I'm actually fine with it, because by then, like you said, Shepard has been stuck with the same aliens for some time now and knows he/she can depend on them whether the trust is there or not (the friendship thing seems a bit forced, but on the other hand I can see why it's there; I think a lot of people just want their squad mates to be Shepard's best friends (yes, I do, too
) and I would think the majority of people would not even consider playing a racist).
Plus they're really in a situation where every help is needed. I found it awesome when my Shep also got over her issues with the batarians and asked for their help against the Reapers, that was such a cool moment.
It's like Ash in ME1, she understands that if it takes working with aliens to achieve something, she'll do it without hesitation, despite being suspicious of them.
What makes no sense is of course if for example Garrus is never recruited in ME1/2 and suddenly acts like Shepard's best bud. One can hope for the future if they ever make a trilogy again this will be taken into account 