See I did not get the impression that Jess has been actively pining over Rory for the last 9+ years. I'd like to think he's been in Philly, had relationships, career struggles, the usual living-life stuff*. Just because we aren't privy to it doesn't mean he or any of the other characters have been in cryo for the last decade.
Rory mentions it's been four years since they last saw one another; considering their familial situation, wouldn't that suggest that if Jess was truly interested, even if in a distant way, that they could've had opportunities to reconnect sooner? I guess I just don't see Jess as that passive a character.
I think it was proximity to Rory, being with his family (Luke) again, and later, the wedding, that stirred up feelings that he had set aside a long time ago. And once he met again with Rory, and heard her pitiful tales of woe, warning bells went off- he knows what happens when Rory spirals down. So it became a head/heart struggle, and come wedding time when they couldn't help but be around each other, he did the healthy thing of remove himself from Lorelai and Luke's house until time to go back to Philly.
*Due to limited screen time (and possible sequel planning) Jess's storyline feels particularly truncated and unfinished; I wished we'd gotten a bit more sketched out about him because what we're left with is pretty unsatisfying.