This is an interesting topic because I think it shows the divide between the rational/scientific and the emotional.
I normally tend to be an analytical and scientific person, but the funniest thing happened to me when playing ME1. I played a Femshep who was annoyed at Liara and her "instant connection!" and who had a hopeless and unrequited crush on Joker. But I also surprised myself by getting a little crush on Garrus, too. His VA is just wonderful, and I loved the character.
Then I played ME2, and suddenly a romance with Garrus was possible -- and my Shep would've probably gone there, but she'd already fallen flat for the gorgeous Drell. Yes, Thane is a Creature from the Black Lagoon. But a drop-dead gorgeous and sexy one. I had no trouble believing there would be a physical attraction there between the two of them, and my Femshep was all in.
Meanwhile, as the game went on, I still found Garrus adorable as well, and while my Femshep didn't quite ever fall for Liara (although LotSB did make me finally warm up to her), she had a total girlcrush on Aria. And -- funny thing -- Nyrene, too. When we first met Nyrene, I thought she was much more stark and alien-looking than Garrus, but by the end of the Omega DLC, I thought she was elegant and weirdly beautiful. I saw what Aria had seen in her.
(Or on a similar note, look at the Charr and his "Blue Rose" -- in ME2, it was played for laughs, but somehow in ME3, that final message of his to her was just so sweet, and her reaction so genuinely sad, that it really got to me.)
So I think the fun of ME, for me, is that we're presented with a universe in which sentience and maturity are all that's required for love between even the most different of beings (especially in a universe in constant danger of ending violently). A Hanar is a sex symbol and action hero! (It still makes me laugh...)
But it's not a bad message, and one thing the ME universe does well is that it reminds us of how inconsequential human homosexuality or bisexuality is, for instance -- especially when compared to the crazy human/alien potential pairings in the ME universe. The game also reminded me of how much of attractiveness can come down to unexpected things like eyes or voices (I love both Thane's and Garrus's voices and think their VAs are outstanding).
I honestly felt that Thane's marriage was failing prior to Irikah's death because Thane was a workaholic, and not because the family was hard up for money either. Initially maybe! But since he was the top assassin in the galaxy I assume he did not come cheap, and after so many years and being away from home so much I assumed that, unless Thane or Irikah were really greedy and needed to live in the poshest of settings, the reason he worked so hard was to maintain his reputation as the best of the best; considering I always saw Thane as mildly arrogant and prideful about his work this is not too far of a stretch for him to do.
My impression of Thane's marriage (at least for my Femshep) is that he fell in love with Irikah, but that it was doomed from the very beginning. They met as antagonists and while he was drawn to her fierceness and goodness, and she eventually accepted and loved him, to me the implication was that she wanted to change him. I always rationalize that he was away so much because he knew that to stay home was to hasten the end of a marriage that had already died, so he just immersed himself in his work, losing his way bit by bit, and stayed away until it was too late and she was actually murdered because of him (adding even more guilt to the equation), and he had lost the chance to raise and know his own son.
What I liked about Thane's story was that it was complex and messy in a way that felt real to me. He had aspects of nobility and kindness (I always love how courtly Thane's speech is), but he was also a guy who was not only an assassin (however he rationalized that), he had abandoned his wife and child and felt tremendous guilt over that. He avenged himself brutally on those who killed his wife but it also seemed to me that he was seeking an absolution he would never get.
I like the way Thane is presented as trying to make amends for his mistakes -- it's a classic and fascinating character approach -- and I do think that his unexpected romance with Femshep is both cruel and kind, as he has discovered the love of his life only at the end of his.