Well, Empire taxes my PC to the limit, so picking up Napoleon probably wouldn't be a hot idea.
Also, Napoleon seems a more focussed, constrained game than the wide-open Empire, which is somewhat less appealing to me
I loved Rome, and initially I was pleased at not having a Pope breathing down my neck, though the campaign AI made it seem much more constrained, as there was no longer such a thing as a secure flank, money was tight, and simply expanding in the wrong direction can ruin your game.

Anyway, the thing I liked about Empire was it was wide open. With no Pope or Roman Senate to get in your way (and a decent campaign AI), alliances come and go, but it doesn't seem random. You can expand in any direction, overseas, fight a neighbour or across the map.

Personally, I'd like a Rome II, though I know it's not going to happen.