What this would do, of course, is to make Elly's daily life look like the one a person would assume it was if "Farley follows his nose" was his or her introduction to the characters. The distinct impression I got when I looked at it is to think that a person new to the Foobiverse would assume that Elly was a single parent who had made her kid brother into a sort of family retainer. Thus would post-John life be like for the first few years; we'd have Michael being the moody mild antagonist and Liz the precocious and protected favourite and Jim standing in for Evie.
As for the antagonist who occasionally emerges to threaten the new status quo, we'd have a ready-made rat bastard idiot: John. Every so often, he'd crawl out from under his rock and try to mess with Elly because he'd convinced himself that she simply cannot survive without a pompous ass telling her that thinking about her feelings is anti-family. We'd spend the months after Mike and Lizzie's visits with Daddy having to deprogram them and every so often, Elly would end up in a court room trying to fend off John's attempts to screw her over.
This would mean that instead of John and Phil damned near dying in order to separate the Early and Middle Years, we'd have to deal with John marrying his ally in the fight to harsh Elly's mellow: Connie. That's right. I went there and I brought back souvenirs. Connie's reaction to the idea that Elly no longer needed her as a failed Jiminy Cricket would be to act like a rejected suitor. The resolution would come when Lawrence told Mike that no, the problem wasn't that he didn't have a 'normal' life, the problem was John being an ass. Once Mike finally got it through his thick skull that Mom and Phil and Grandpa Jim were right about what a clod Dad was, we could thus proceed to the next phase: Elly deciding to re-enter the dating scene.