AttemptToCallNil, it sounds like one of your major gripes and thus reasons for thinking that Fandom Inc. has been more accommodating to Fandom wikis is that they aren't taking enough feedback and/or are manipulating survey results by closing polling. Those of us here on Fandom have faced a similar frustration with a lack of transparency/answers regarding the migration. The fact that Fandom started first does not mean that Fandom somehow has inside information that Gamepedia does not.
Overall, I think the migration will impact Gamepedia wikis less than Fandom wikis. As you said, Gamepedia is not jumping 14 software versions and losing a ton of custom features. That said, I find it hard to believe that Gamepedia would keep the current layout in the long run. Perhaps in the immediate future it will, but part of having a "unified" platform is having a uniform look. As for the social features, I would imaging that Gamepedia would have an option to just turn them off; I am pretty sure Fandom can. So in the end, I think both Gamepedia and Fandom will have significant changes. However, I believe that a larger portion of Fandom's changes will be actual functionality compared to Gamepedia's changes.
Edit:
By the way, has there been any word on what will happen with interwiki maps on Gamepedia? As far as I am aware, Gamepedia and Fandom have completely opposite approaches. Gamepedia allows admins to edit and interwiki map more or less however they want while Fandom requires admins to submit a request to staff which may or may not get approved.