The team do want to move on to the next game more then anything, no point in being stuck in Fleeting Iris forever.
Expect more animations in the next game
Well, I would too if I was stuck in an ancient engine for over half a decade.
I know they had this project as an 'infinitely ongoing' game for all that time (and to be fair, many DEVs do that), but honestly I wonder why DEV teams don't just 'finish' their games with a smaller scope & split them up into 'parts'. Basically what Monster Girl Quest does.
The way I see it, you have a finished product you can sell (quicker), but mostly you can switch/upgrade engines in the middle.
You'd be able to get off VX Ace, up the resolution & stuff like that w/o the need for recreating or upres'ing the whole thing if you would wanna upgrade engines in the middle of maintaining an existing product.
Now ... it doesn't prevent a full interlinked storyline, but I guess it would end up with some overhead at the start of each 'iteration', such as recreating/upgrading the maps if you want to reuse them.
That kind of release structure does have an impact on how you tell your 'story' though. So when you rely heavily on the 'route' concept like this game seems to be doing, it might not be so easy. You'd end up with Part 1 having routes A, B & C. Part 2 then getting D, E & F or something like that, which might also not be ideal.
Heavily scripted games ... it'll probably be some work when switching from the proprietary VX Ace script thingy to modern JS (though I would expect them to have that work for the next game now, since no doubt they'll want to try and transfer some features, and I'd also assume they won't go for the ancient VX Ace engine anymore at this point).