Actually the problem with the dynamic between Jerry and everyone else is even worse than that. At first everyone except Rick is more or less normal. Over time Rick "converts" the family to his way of thinking: first Morty, then Summer, then Beth. Jerry is the only one who doesn't abandon his "stupid" values and accept Rick's vulgar nihilism. In spite of Jerry being described and portrayed as weak and pathetic most of the time, he's the only character who puts up serious resistance to Rick's manipulation and abuse, not just among the family but out of almost all the characters in the show.
A lot is made of the Rick/Morty relationship, but the Rick/Jerry relationship is a lot more revealing about the characters and the writers. There's a real Yin/Yang dynamic going on here. Rick is the Yin (masaculine, active, dominant) and Jerry the Yang (feminine, passive, submissive). They pull the family in two different directions and oscillate between extremes, but more or less exist in balance. And like the Yin/Yang symbol each one contains a piece of the other. For all his power, Rick has major vulnerabilities at his core that he sees reflected in Jerry to great irritation. At the same time Rick sees a bit of his power reflected in Jerry that allows Jerry to resist his control and maintain a separate identity. This dynamic is less about interpersonal relationships and more about internal conflict (mostly Dan Harmon's). How the two men interact with their family and the rest of the world shows how Harmon sees people's interactions.
Rick is always bent on "winning" and controlling every situation. He's obsessive and paranoid, and he has found a way to justify this behavior by actively involving himself in conflicts that require this mindset. Rather than try to change anything about himself, he tries to change the world to suit him. It's like the first line in The Departed - "I don't want to be a product of my environment. I want my environment to be a product of me." It's the logical conclusion of Will To Power, to become as God and transcend the world you live within. It's Rick's ultimate inability to ascend and his fallibility that create his massive insecurity and vulnerability. Because Rick is the ultimate Übermensch, he can't accept this vulnerability and takes every precaution to repress and hide it. For all his bluster, he's still quite limited because he can be bested by Jerry. It's the whole God vs Free Will thing. Sure, Rick could kill Jerry or use some pheromones to control him, but that's still "losing" because he's not bending
Jerry's will, just going around it. It's like a reality check that Harmon has when he meets someone who won't kiss his ass and call him a genius, no matter how hard he tries to impress them.
Jerry just wants to go along to get along. He's avoidant and skittish, but he does try to recognize and deal with his flaws. He knows he's no match for the universe or for other people so he's perfectly ok with compromising and meeting the needs of others. A deeply understated aspect of Jerry's character is an adaptability that rivals Rick's engineering skills. As much as the other characters take weirdness in stride, they tend to be detached from the shenanigans around them (opting to use superior force to get what they want) whereas Jerry learns the ropes and makes friends immediately, integrating into the situation instead of acting on it as an outsider. Jerry might settle for minimum effort, but in situations where minimum effort is high, he rises to the occasion (like the original Jerry in the Cronenberg universe). His method also tends to work
, which makes Rick hate him more. He can best be summed up by his own line, "I just kept crawling and it kept working." If Rick represents how Harmon sees himself at his best, as a master of his craft, Jerry represents Harmon where he is incompetent (especially in dealing with people). However, like Harmon or anybody else, Jerry has a spark of willpower, and like Harmon (but unlike many people) he holds onto it with a death grip so he can use it when he needs to.
The two tendencies are always fighting each other because the nature of each prevents them from ever reconciling. Rick won't accept defeat. Jerry won't push the issue the way he needs to. Maybe in real life Harmon could learn to integrate the positive aspects of both of these archetypes, but in the show they are contained in two separate characters. Morty and to a lesser degree Summer synthesize the two sides, but as long as Rick and Jerry are present in the show, the conflict will continue. Past a certain point it kind of becomes tedious and honestly I just lost interest in the show because the What Ifs were not that interesting and the character drama had played through pretty much all of its possibilities. In an alternate (socialist) universe the show might actually resolve/evolve the dynamic by giving these two characters major development, but in capitalism the show's brand is too fixed and the fanbase is too attached to the established characterization for challenging the audience like that to be allowed. Even if Harmon wanted to take it that direction, the producers would veto it because of muh bottom line, even though the show has already made them all rich(er). They all see themselves as Rick, master of the system but that's really much more a Jerry thing to be, because it's a closed system and they are bound to its rules, where Rick's whole thing is transcending a system and making it do what he wants.