My problem with Jon/Dany is not that I think such a couple would be cliché per se (in fact, I can't even think of a an already existing compareable fictional couple right now; many people bristle at the notion of pairing the ostensibly most heroic guy with the ostensibly most sought after woman, but since I don''t think Jon is necessarily more heroic than Davos or Sam or Mance and Dany's desireability is hardly her defining feature, I have less of a problem with that) - I just fear that it might be entangled with a lot of other plot developments that I would find very cliché (eg. Jon Starkaryian, Dany as Nissa2.0 and such things).
There are three potential forces that might pull Dany and Jon together:
a) politics: only works if Jon's true lineage becomes common knowledge. I don't want that to happen, so I'm of course against a Jon/Dany marriage based on political considerations. And yes, Jon Starkaryan, the hidden heir who saves the day and takes the throne would be horribly cliché in my eyes. Let him save the day (in collaboration with a lot of others), but keep him off the throne for the sake of the old goods and new.

prophecy: I would hate that too, because I hate the idea of Jon and Dany slavishly executing their respective prophecies. I want their heroism to be motivated by a genuine concern for the common good, not because they are f'cking chosen ones. A rehash of the original AA/Nissa-Nissa story would be the very definition of clichéed for me.
c) genuine attraction: as a member of the apparent minority of fans who are equally fond of both Jon and Dany, I could actually see them growing to genuinely like each other - but it think it would take quite some time and I'm not sure there will be enough opportunity for them to interact with each other to plausibly and organically develop such a relationship. But who knows... I didn't think Martin would ever make me like Jaime or Theon either. He's a f'cking wizard.
While my objections to a) and

are mainly ideologically motivated (I don't like what such plot developments would say about the importance of free will and the importance of bloodlines), c) is an objection on purely aesthetic grounds. It's the only option in which a Jon-Dany-pairing could feature under the subheading "romance" and I just don't like underdeveloped romances and would rather have none at all than a half-hearted one. So far Martin has not developed any plausible attraction between Jon and Dany (which would necessitate having them interact with each other in some way), so I remain sceptical for the time being.
I would probably okay with it, under a following conditions:
a) it doesn't lead to marriage

it doesn't lead to AA/NissaNissa
c) it's not rushed if based on genuine affection
d) it's not sold as a romance if based on mere physical attraction