Though I like the idea in the case of a single ship, I'm not sure this would make sense for entire fleets. Considering the complexity of control and organization of a fleet, it makes sense to me that the resulting effect of a gravity well is the loss of open space bonus speed. We don't want our brawler frigates flying into our hammerhead cruisers at 1000000 miles a second. Take it slow, take it safe.
I do think that smaller fleets should be less affected by asteroids and gravity wells. But really when it comes to the coding, the system map movement is not the heart of the game. Whatever time gets put there we lose out on economy/diplomacy/PC AI.