I felt like sexuality could have been handled better, but probably for different reasons than you.
I thought Joker/EDI and possibly Tali/Garrus were nice changes from the "everything revolves around Shepard" approach. I could even see there possibly being a hint of Vega/Ashley.
Joker/EDI isn't about all relationships with robots being accepted - since AI's are illegal (or at least very, very tightly controlled) and VI's seem to be little better than a holographic GUI for a regular computer. As others have said, it was a play on Joker being in love with his ship, only in this case the "ship" is, through the actions of himself and others, able to love him back, as well as a vehicle for EDI to learn about humanity in general.
The lack of reaction from ME1 love interests to finding a new one in ME2 bothered me quite a bit, but I don't think it has anything to do with the character doing something they find sensible - I think it was just not allocated enough resources during game development. Similarly, if you stayed faithful, I think it should have changed things up dramatically. For example, I romanced Ashley but stayed faithful in ME2 - I expected that when she came on the Normandy after healing up, she would come to the Captains' quarters. Okay, failing that (2 years isn't a short amount of time, after all, and then Cerberus) they should have had some meaningful conversations. The thing with Ashley's sister was nice, but once she was on the ship, it felt like there had never been anything between them right up until she came up to spend the night. From what I hear, the other romances were handled reasonably similarly. That's very disappointing to me.
Cortez's being outed was, I thought, handled with perfect clarity and simplicity. As others have said, Cortez is a good guy and good pilot who has issues with letting go of his past love. You gradually help him over it. That love happens to be male, so he's gay. His initial statement about having lost his husband was very straightforward and also made his orientation perfectly known. Now, I find it a bit icky that if you play a gay Shepard, you can help him out and then immediately start up your own thing, but that has nothing to do with being homosexual - that's just possibly being predatory.
I notice you don't mention Traynor (or at least I didn't see it, if you did, then I apologize). I thought Traynor was handled with a much defter touch. From her brief mentions of liking EDI's voice and . . . uh . . . some overheard conversation she had with Allers over the intercom (I don't remember exactly what was said, although I do remember that I got the distinct impression she may be into girls), you get an impression, but she doesn't clearly state it until she's in your cabin. I thought it was much more fun that way, although it does make me wonder. Were Cortez and Traynor just different people, with different issues, or were they intentionally written differently because being gay is perceived as less acceptable than being a lesbian? If Cortez had played things much more subtly, how many angry people would be complaining about being "tricked" into being gay? If Traynor had been more forthright, how many people would complain about her being "butch" and "in your face"? It's unfortunate. But I liked Traynor's character, and I liked her more subtle reveal - which was not a case of her necessarily hiding it (although it could be perceived as such). I just thought she was naturally a bit more reserved and less inclined to talk about such things.
Although underwear in the shower scene? Really? Lame. I don't demand full frontal or anything, but come on, now. Use some tasteful arms or hugging or turning or something to conceal what you feel must be concealed, don't just leave them in underwear. This applies generally to all the sex scenes (except Liara's, I guess).
The woman cheating with the asari didn't seem to be written any differently than if the asari was a human male, or male of any other species (or female of any species). It was a little story about a married spouse who decides to leave their partner for their piece on the side, and about said piece on the side being okay with the leaving if it's due to longstanding issues, but not wanting to be the cause of it. I didn't get any sense that it was acceptable - the cheating was reprehensible and the leaving possibly so.
So, to summarize, although I wasn't happy with how being faithful was not really treated any different from cheating as far as the relationship progression was concerned (save one or two different dialogues), on the whole I thought the relationships and characters presented in the game were reasonably solid. They were about people and relations between them, not about their orientations. Would I have liked to see, say, Liara coming up to Shepard's cabin to sleep, rather than staying in her Shadow Broker Information Center, at least once in a while? Would I have preferred to see some sort of "date" between Ashley and Shepard, eating military rations in his cabin, trying to reconnect after two years? Absolutely yes. But, that's not where BioWare chose to put its emphasis, so whatever. Which I find interesting, in comparison with your view that you were playing a love story. When facing total war and the annihilation of everything and everyone we care about, I think relationships between people can be a very interesting story to tell - that doesn't make it a dating sim, it makes it a case of science fiction examining the human condition under fantastic circumstances, which I feel is a great thing.