Lance brings a running element that JG did not have and he also has a bigger arm. So he'll be a big upgrade in those areas. But the one thing that made JG a good fit for the Shanahan system is his quick decision-making ability and quick release. Lance has a long, looping throwing motion that telegraphs passes, which will give defenses more time to react, and also result in more batted passes. In fact, I heard it stated somewhere that Kyle Shanahan wants Lance to work on his throwing motion this off season, so they clearly view it as a problem, as well.
I expect it will take Lance at least a season to get up to speed on the system and it remains to be seen if he'll ultimately be a superior QB to JG in the long run. My hunch is that he won't be, just because it seems like they're trying to fit a square peg into a round hole, but we'll see.
