That's fine in theory, but in games, as in life, "you go to war with what you've got." If war comes unexpectedly, you will find yourself with ships as yet not refitted to the latest designs. With a large game with a large, wide-flung fleet, you may have a lot of different characteristics. So a mismatch of vessels with different speeds is going to be the rule in fleet formation. And that is why the game badly needs to limit fleet group movement and keep fleet units together.
Yes, a very good point: the "living universe" aspect of DW would have one relying on mixed older and newer tech warships with variable speeds. A simple solution (well...simple to suggest but implement?) would be to have an order to fleet move at the speed of the slowest ship.
The other suggestions are good though with a large empire and lots to coordinate, they're rather out-of-character for a macro-level strategy game; just a bit. In smaller games, it would be simpler to coordinate all the ships, rallying point, targeting, rapidly scanning your speeds, etc.