With the update of the sector space looking like you're actually traveling, obsticals would be a great addition. Toss a nebula (class dangerous) in the middle of a sector. You could either autopiolet and the system would stear you around it or you could go as the birds fly and risk a mission inside. Traveling ion storms with the same effect. (your warp engines become inefficiant and you have to go warp one or you have to wait like they did in Enterprise and that one episode in DS9.)
Where this stuff didn't seem like a good idea in the old sector space, in the new it would be fantastic. But keep in mind that the dev's have a thanksgiving dinner of issues in front of them in the first place. I hope they add it as it is a great idea, but I'm sure it won't be for a while.
Doesn't stop you from drawing a mission in the foundry which can simulate the results of a nebula encounter. Make it great and maybe they will use it if they do implament your idea.