Sector Space doesn't have to be removed from the game... just moved to the Astrometrics room aboard your ship. You want to do DSE's you walk youself through your ship to Astrometrics and select the encoutner from there, whether it be PvP, PvE or even PvPvE.
Normal, sector navigation should be from the bridge. Trips should take much longer to get from system to system but to make this faster major sectors should have a Transwarp Conduit. They appear in a few places already and the network has been mentioned so it does exist... somewhere.
This is basically my stance but I favor doing exploration clusters from an Astrometrics/sector space view, just replacing the ship with the astrometrics platform.
On the whole, I think what people dislike about sector space is that it's a metaphor for space with your ship seeming to float in it literally.
With astrometrics/stellar cartography, we have a very similar metaphor for space in the canon. It makes sense to me to do the exploration clusters from there, just replace the ship paper doll with the Stellar Cartography platform and the framework of the room itself.
I think this makes sense for navigating exploration clusters, complete with the grid and even lollipops if they add some persistent elements in those sectors down the road. In fact, exploration from the bridge makes little sense to me in the 25th century. If you're discovering new and uninhabited planets at this point, it seems to me that the person who does the discovering would be in Stellar Cartography or an Astrometrics lab, not the bridge. You'd have to be an idiot to run into an unknown planet especially one near heavily charted space, with what's available on the bridge at this point.