I prefer a slightly more hands off exploration mechanic than is often used. I don't want to spend part of every turn scrolling around the map looking for the different units of my scout fleet, or forget to move something for a turn.
I want big marker icons "Current missions: X% complete". I want to pick the region that I'm interested in learning more about, and decide how important it is, which in turn decides how many resources can be devoted to completing the project, which then affect how many turns it takes before I get my next bit of detailed info on it.
For a strategy game like this I would rather have a good idea of the layout and some probabilities of what a star system has from the get go. (Just seems odd that I don't even know about a star a few lightyears away, let alone not having a clue if it has any kind of planets or anything.)
I say keep exploration, but keep it to budgets, targets, and technology decisions. If I'm the emperor then it really isn't my job to say if S-108 'Victoria' is sent on the mission, or if S-109 'Intrepid' goes. A ship, a few ships, or a lot of ships is what I want to choose, and I don't care where they come from, but I would assume my admirals would pick the most logical ships to allocate to the project.