Save files were literally the first item in the issue tracker, but sorry to say, they're not fixed yet. There needs to be a way to get them to play nicely with AngelScript (and other engine changes, but that's the most obvious), and because there are no SP episodes that explicitly require JJ2+, it's never been a priority.

Jelly Jam: Ideas from the community certainly get used sometimes, but they have to hit that sweet spot where ease of implementation meets definite benefit. No guarantees on any specific suggestion.