You're right that people make jokes about it now, but in order to make a convincing argument you have to more explicitly connect the nature of those jokes to negative buying intent. Are the people making jokes the same people who want the game? If they are, does the fact that they make jokes imply they no longer want the game?
"Negativity" is a broad concept and I don't think the kind of negativity you're citing is necessarily the type to change branding over.
As for Versus distancing itself from FFXIII, I think that's a reasonable observation, but not an analogous situation. FFXIII has an established (negative) reputation that was worth distancing. It also cost them very little to ditch "Versus XIII" which means nothing, and replace it with XV, which means "This is a real, main-line FF game so get ready." Most importantly, it's still called Final Fantasy.
TLG's reputation, on the other hand, is mostly positive expectations due to the studio's past work, which you might adjust in consideration of its development hell, but again, only knowledgeable consumers know the game's development history and a name change won't affect their perceptions.