Part of it's to do with intention, I think.
Sam/Gene was subtext - was always going to be subtext - was there simply as an homage to buddy cops and accidental due to Phil and John being able to smoulder at each other.
Gene/Alex is intentional, and blatant, and over the top, and overused.
But the most important thing is that it's the only sense you get from Gene and Alex's relationship.
Gene's attracted to Alex, and Alex is attracted to Gene. That's it. You don't see Gene's growing respect of Alex as a police officer, despite distaste at her ranting and techniques. You don't see his trust in her --- they keep saying we would see another side when he's with her, but haven't yet, and we'd had two significant and open dialogues between Sam and Gene within the first four episodes of Life on Mars. We don't see Alex's trust in Gene, either - which with Sam was always a different type of trust, but vital nonetheless. We rarely see Gene doing the give and take routine with Alex, nor her informing his decisions. We don't see Alex acknowledging that maybe Gene has a point or five. Their interactions have had no progression - they've stayed pretty much the same all the way through, whereas with Sam and Gene, there was a build up. You don't get any sense that Gene likes Alex as a person, only as a bit of skirt --- and why would that be the basis of a relationship you'd want to write about?
The reason Sam/Gene is my OTP is because there is so much in their relationship. The conflict, the comedy, the caring. They fight and they laugh, and they love each other (and yes, I've said before, in the show, it's platonic, but so clearly there.) They need each other. But Gene and Alex... want each other. It's a simple and easily defined relationship and it doesn't interest me. It's just sex.
And, it's a perfect representation of the whole show. That when I'm being negative, I can highlight as one of the main roots of the problem. It's just flashy, just nostalgic, just a television show. The small amounts of depth and subtlety are wonderful - but not there enough. And I'm enjoying it, because it doesn't affect LoM for me. I thought it would, but it doesn't. All it really does is impress upon me even more strongly exactly how amazing Life on Mars was, despite an ending I will never love. I'm not having the same emotional connection on any level. I can't even be bothered to hate it.