After this weekend, I am of the opinion that Shafer is in the right place.
The reason why I say is, I just got done playing Civ IV three times, with all of the expansions/patches. This is after I played Civ IV once a few years ago, shortly after release. It's a much better game now. Lots of cool new civilizatons, natural disasters finally got added in and they're not unbalancing, lots of little bells and whistles. I understand that Shafer was there through all that.
Enter Elemental. Elemental is in pretty much the same position that Civ IV was then: much-touted, but the release did not go so well. And then Brad committed to improving it. Regardless of Jon's role or his success with it, he has experience with precisely this situation. I expect Elemental to go pretty much the same path as Civ IV: a good game, but a little late to the game. Where things start to get really interesting is what happens after that.
My impression of Civ V is that it was a natural follow-on based on the feedback Civ IV was getting. Civ IV was a good game, but it simply takes way too long to play. Too much micro, and too often you have to choose between doing the micro or simply not playing as well (Galciv2 was worse in that area, BTW). The worst part is there are no good stop-off points. When do you hit "Save Game" and go to bed? In Starcraft 2, that's easy: when the mission is over. But in Civ, "End Turn" is actually one of the worst moments to call it a day. So when do you??
Civ V took this sort of feedback and made a sequel attempting to digest all this input. It may not have done very well with it, but I probably would have made all the very same mistakes they did. It's okay to fail sometimes. The real question is, are you still in the game? Jon is, and he's at Stardock now. Good luck, and I'm pulling for you. Not saying I'll buy your game, but I'm pulling for you.