... do you think the notion of forcing Mat to trust Tuon to return at the end of the Last Battle is supposed to be related to this desertion?
Pretty sure this was to be the case. I think it would have begun with Mat having to become peacemaker between Egwene and Tuon. Which he did, but by making it a one line comic cameo, the thematic implications were completely lost.
The arc should have been:
1. Mat abandons Rand, Egwene and Elayne to go to Tuon.
2. Egwene and Elayne keenly feel betrayed. Rand decides it doesn't matter and confronts Tuon (and Mat), forcing them to do their part.
3. Things go to shit for the Aes Sedai, and Egwene has to make the difficult decision of not just trusting Tuon, but forgiving Mat.
4. As things go further south, Egwene (and Elayne) have to make the difficult decision of leaving the entire Last Battle in Mat's hand. This decision should have been a lot harder for Egwene, given that Mat had become a Seanchan prince, and abandoned the Randlanders to go to Tuon. Her deciding to finally do it should have been about a lot more than simply trusting Mat because she knew him as a kid. The aspect of essentially surrendering her fate to the Seanchan to control the outcome of the war was absent, which was absurd.
5. Mat himself should have had grave doubts about what he was being asked to do. He has been resigned to some level of duty for a long time, but here he was offering to take the fate of the entire world in his hands. This was another massive decision that was presented underwhelmingly.
On the whole, the Seanchan-Mat-Aes Sedai storyline was one of the worst.