Gunn doesn't deserve him anymore.
This is, alas, all too true. And yeah, I loved your portrayal of Lilah, Plei - sorry, should have said as much, but I was all choked by the Gunn! And Wes! wistfullness. Sigh.
See, my own reading of canon, fwiw (I mean, canon-in-the-head-of-Fay) is that Wesley had the hots for Gunn, but never did anything about it - because although Wes isn't exclusively in the vagina business, he was quite sure Gunn was, and he was still a little backward about coming forward in matters of the heart, or in things that mattered deeply to him. In point of fact, Gunn did have these burgeoning feelings developing for Wes, but he was all kinds of not comfortable with them and trying to ignore them with variable degrees of success - because, man, he just loved Wes. Seeing Wes made him happy. They were practically dating in all but the actual, er, dating part of it. And in my version of the Jossverse, Wesley's sexual orientation had cropped up one night when they were out having a post-slayage drink or two, and that had been a little fraught, but Gunn had, whilst freaking out internally, said "yeah, okay, cool, whatever" and started to realise that maybe his own feelings for Wes weren't entirely platonic. There was all this trembling potential hanging there between them, and growing intimacy, and trust, and all that lovely stuff that Shrift evokes so well in Comfortable.
And then Angel came back, and the group dynamics were in a state of flux again. Wes was the boss, and Gunn kind of liked that - because Alonna's death made him lose his taste for giving orders, and he was proud of Wes, and all kinds of pissed at Angel. But there was a little touch of awkwardness then, with Wes in his office alone, and with Wes lighting up whenever he saw Angel - 'cause Wes has been carrying that particular torch for quite some time. Gunn didn't like that so much. And Wes had absolutely failed to realise that Gunn was starting to fall for him.
And then George died. And that hit him hard, and left him with his heart in his mouth and a sense of freefall and failure and divided responsibility - but he followed Wes, because at the end of the day he couldn't let his boy go off to some Hell dimension without him. With Angel.
And then - Pylea. The old Wes'n'Gunn thing was back, comrades in arms, shit hitting the fan, yadayadayada. I think Beast!Angel got a pretty good whiff of the pheromones going on there, because he went for Gunn, and as far as I'm concerned that was territorial. Wes was supposed to be his faithful servant, thank you very much. But I don't think anything had happened still - I think it was just all USTy.
But in Pylea Gunn saw a side of Wesley he hadn't really seen before, I think. Wesley can be one ruthless sonofabitch, and is prepared to make calculated sacrifices - and this has been clear right from the beginning, back on BtVS. It's something Gunn has never been good at. Ironic, that - because Gunn thinks of himself as being the stronger of the two, but he's got a streak of tenderness and pliability where Wes, unexpectedly, is steel. (In this and in much else Fred is very like Wes. And it's the reason they both fall for Fred, surely.) Gunn was taken aback, and not wholly comfortable. He's got too many deaths on his conscience already.
I don't think that Wes realises even now that he could have had Gunn. That if things had been just a tiny bit different, he could have had him. But Gunn knows, and it freaks him out. He's not comfortable with it at all. And he knows, whether he admits it to himself or not, that part of the reason he loves Fred - not all, no, but part of it - is the way that she echoes Wesley. The way she's an acceptable version of Wesley. We aren't talking Lilah-wearing-glasses-and-braids, but the big old brain and the glasses and the fragility and the strength - these are things that draw him. He's just now realising that she's ruthless in the same way that Wesley is ruthless.
I don't think he realised that Wes had fallen for Fred, but when he did, he felt guilty and jealous both, and, as we do, he reacted to the guilt by blaming Wes. Eventually by lashing out at Wesley. I mean, jings, there's no way his actions are forgiveable - siding with Angel, with whom he said he'd never be friends, over Wes. Especially when Wesley's decision about Connor was so thoroughly understandable. Gunn has made bad calls in his time - hello, Mr Sell-your-Soul-for-a-truck - and Angel didn't harbour rage about Wesley's actions to the degree that Gunn did. Which says a hell of a lot.
signed: Thinks Too Much About This Stuff.