The only reason Factorissimo2 exists is because Factorissimo1 was originally written as a proof of concept in a single weekend, without any consideration to performance, aesthetics, code quality or maintenance, and as such it had some major flaws that made an incremental update completely unfeasible, leading to a complete rewrite and rerelease with a new mod ID. But now that Factorissimo2 has decent code, there is no reason for another complete rewrite, and any changes or new features can be added to Factorissimo2 directly.
I'm curious what kind of major changes you have in mind. Why not suggest them? If I think they're sufficiently neat and fit my vision of the mod, I might just add them to Factorissimo2.