I know it's been PAGES, but ...
Obviously I'm viewing it through a straight woman lens, but I found the ManShep/Kaidan romance superior to the FemShep/Kaidan one, in part because you couldn't romance him until ME3. My "canon" ManShep started out romancing Ashley, but he shed a manly tear as he rescued Kaidan instead, and he had no good answer when Kaidan angsted about why. By the time I got to the end of ME1, I remember thinking, "You know, it's dumb I can't get together with Kaidan. It just works, somehow." Their fight on Horizon seemed just as charged as my romanced-Kaidan FemShep's fight, which reinforced my "Seriously, they'd be adorable!" leanings.
And then in ME3, they finally realize they've cared about each other that way all along, which is a trope I can be a sucker for if it's done right, and I think ME3 did pretty okay with it. They just sort of slot in together, in a way that makes you think, "D'awwww." It was probably the most organic-feeling m/m romance I've done in a Bioware game (although I heart Zevran forever and ever and ever, the whole he-tried-to-kill-me thing puts a teeny damper on the "does this make a lick of sense" front.). No dead spouse, no weird baggage, no attempted murder, no zealotry, just a bit of an entirely-justified trust issue that gets resolved before it gets annoying.
There was also no whining I cheated on him. That was a big plus. 
On the WHOLE, I like DA's romances better. But I really have a soft spot for Kaidan/ManShep! 
Hi, um... All of this. ALL. This is EXACTLY how I feel about male Shep/Kaidan. My (unrealistic) hope is that Inquisition manages to pull something off as sweet as that pairing. I know they've only got one game to work with instead of three, but man, I hope they try. Male Shep and Kaidan are probably the biggest reason that the ME franchise stands out like a beacon for me amongst all the other games, with the exception of Dragon Age.
I thought the "struggling with sexuality" story was one they wanted to do but couldn't for this game and had to put on the backburner?
Huh, really?? Well that's a shame, if it's true. I think a "struggling with sexuality" story would be really great. Not sure how well it would fit into the world of Thedas - where we've never, ever seen anyone persecuted for their sexuality in the first place. But still, I would highly enjoy something like that.