It's terribly saddening that Flynn has had to abandon Stray Incubus. It was one of the handful of VN's here I was able to see the progression and improvement throughout.
The conundrum of whether someone should takeover or try to continue SI reminds me of other Abandoned games, as well as TV shows when the original writers are replaced: it is so incredibly difficult to retain that feel, whether it be the humour, the sex scenes or the characterizations.
My idealistic suggestion in what to do would be to treasure the memories of this game and its characters, and perhaps to have some cameo in other games - think of how many other VN's Misty has appeared in. That might be the best way to appreciate Flynn's work.
Bringing up TV shows does make me wonder of a concept where AVNs are made as a season/franchise with different devs per season, like how shows have different writers/directors per episode, sounds interesting but also no guarantee if they'll feel like the same game/have the same quality
Considering the world and lore of SI it would be interesting to see pan out, but I do think that's better done on a new piece of media rather than trying to continue someone else's work. I agree on the sentiment that the game should just be put to rest rather than try to be revived, as sad as that may be.
That being said, considering there are games that are straight up parodies of mainstream media but are good enough quality and characterization to stand on their own two feet, I can see a possibility of making a completely new game but with the same character models, like how Flynn used Luna and her dad from Eternum, and the Stormside girls, but gave them a twist here to where it feels like they're alternate universe variants pre-existing in this world.
Like the game could be Stray Incubus: Rebooted and just carry on the storyline with some new flavor, but that would take a pretty good writer to actually be received well imo.
Another direction would be to have like a reincarnation/alternate universe where the same characters exist, either in the same era, or in a more modern setting but have the same lore and story (Percy Jackson style), don't even need to callback to the original game, can just have it as a standalone thing, or if they want either tie in to the plot (like Sicae/MBML), or just have easter eggs (like OiALT/Eternum)