The gameplay and graphics may feel quite different if toggled from overhead to isometric. Would players readily identify it as the same game? Or consider it to be a similar game?
I would imagine it would be viewed the same as any port to a mobile device.
I think it would be better to focus on one style. A cut down mobile version of the game can be an optional follow on project, based on how the original is received. Perhaps game speed needs to be reduced and the FOV made narrower in accordance with the lower resolution and size screen of the mobile device? If so, the entire game may need to be rebalanced/reconsidered on the mobile platform.
There's a chance to capitalize on the release of Phone7 though, which I'd love to do.