Remember "Beast with a Billion Backs"? OK, now that I've jogged your memory have the suppressed images come back to mind? That film reset every major character relationship in the entire show. Yet another reason it sucked, in addition to being a really transparent author tract on polyamory.
I started responding and this got long, so, apologies in advance....
I don't think it's fair to say it reset any relationships. Amy has always been promiscuous and easily manipulated, but as far as we know has been completely faithful to Kif, and did think he was permanently dead. Despite Kif's anger over her affair with Zapp, by 'Green Yonder' it was clear that he wanted her back, and the ending set us up to believe they are together again.
As for Fry and Leela, there are constant scenarios throughout the continuity where it seemed obvious they cared for each other and wanted to be together, but one or the other pursued another relationship instead. Think of "The Sting" or "Devil's Hands", where we're taken out on very poignant examples of how close they are, only to be followed by "Bender's Score" when Leela has no compunctions about going after 'Lars'.
That same fickleness about relationships (you know, like what happens all the time in real life) have been going on throughout the series, which is why they're in a dangerous position now. The Fry/Leela dynamic is easily one of the most significant focus points of the show, which is why I'm afraid the authors will be compelled to escalate their relationship, which could easily be disastrous.
I enjoyed all the movies a great deal, so I can't agree with you about "Beast" sucking, but I think the writers' intent was to cover both sides of the issues of polyamory and promiscuity. Depending on your perspective, you could read it both ways. Obviously one perspective is to see how happy Universe Gamma was and assume it was a pro-polyamory (or anti-jealousy) piece.
Myself, at no point did I perceive Yeebo as anything but an antagonist, and assumed Bender's demonic army plans were meant to give him the Anti-Hero attitude that he does so well. I thought his closing statement of, "There is no great love without great jealousy!" caps everything off and reverts the continuity appropriately, as long as you were prepared to assume that human happiness is *NOT* always the highest goal.