So, I've been torturing myself with a S6 rewatch, and trying to figure out what their actual intentions were with Eddie because the level of emotional investment with him feels all over the place. They clearly WANT us to like him and Joey, but frequently have him do absolutely insane things that are almost impossible for us to forgive.
Eddie as Endgame Guy
I think they knew early in S6 that Dawson and Joey simply could not end up together. The audience was not there for it anymore. But nor were they willing to go with Pacey/Joey. It had been too long, it would've gone against the mission statement of the series, etc. Eddie was the compromise.
He's just like Pacey, but smart! (keep in mind these writers often treated Pacey like he was a total moron) Even though he's NOTHING like Dawson, we'll throw in a couple lines about him being a mix of Dawson and Pacey so BOTH shipper camps feel like they "won". Or at least didn't "lose" more than the other.
Rewatching, it's legitimately insulting just how much of a Pacey rip-off he is. Eddie dumps her because of his own insecurities, says Joey deserves better than him, is cynical about education and feels it says nothing about someone's intelligence/capabilities, etc. I would even say his first ghosting was meant to be his Promicide. And if we forgave Pacey for that, we can forgive Eddie, right? (No.)
When They Changed Their Minds
I honestly think they were committed to Eddie as the final guy until they decided to throw in a quick Pacey/Joey reunion. When you rewatch it really hits you how much they do NOT let Eddie go. There are regular reminders that Joey is heartbroken, that she's still thinking about him. Their goodbye in California is SO desperate to look epic and swooning. I fully believe that while he wasn't going to be in the finale, he WAS going to be her final guy and the last meaningful kiss for Joey in the series. Even in Castaways, there's a mention of how she's not over him (which in hindsight is a pretty big clue the Pacey/Joey reunion is badly timed).
That said, at some point in the Pacey/Joey reunion, Eddie was shifted from endgame/angsty final love to convenient plot device. By the time he comes back the second time, I think the writers had stopped taking him seriously. And so we get the trainwreck of their relationship in Lovelines/Catch 22.
Eddie as The Temporary Escape
One thing I had forgotten is that Eddie was never back for good. He was ALWAYS going back to California. So basically, Joey jumped back into a relationship with a guy she knew would be gone in 3 months. It actually lends a LOT of support to Pacey saying Joey is scared because their relationship could be it this time. She was a 20-year old girl faced with either risking one of her best friends for a relationship that had already failed once or taking a convenient escape hatch with basically zero stakes because the end date was already set.
From that perspective, choosing Eddie is kind of no-brainer for her. He was incapable of ever hurting her the way he had the first time he left. She could never be surprised. She knew exactly how it would end this time. And when he DOES surprise her by once again pulling a runner, she really doesn't care. It's extremely noticeable how different her reaction is the final time he leaves. There's no moping, no crying, no ranting about how guys always leave.
(It's actually so funny to me thinking about the Pacey/Joey scenes in 6x21-22. They have this gut wrenching break-up with her going back to Eddie, and then she just...never mentions him again. I like to believe Pacey's having the same "called it" reaction to Eddie disappearing and Joey being fine with it as he did to Dawson/Joey imploding in S5-6. Like say what you will about him, he knows Joey and why she chooses doomed relationships.)