Ummm, I prefer the interface on IV, probably the technology too, and the ship design was easier if a bit arcane, and I probably preferred the looks of everything to, shipsets were certainly more plentiful...
SEV has realtime combat without an obvious grid, it is also 3 dimensional, but that doesn't really count for much unless you are suffering from bugged ship positions, I have had 30-odd ships stacked one on top of each other before... Ships tend to converge, so they are usually more concentrated. Wall formation is still pretty much universal, you can try to set up weird stuff with pickets and whatnot, but that really just ends up with your ships being out-concentrated... Ships don't get in each other-s way so much, OH, and boarding craft exist, they launch little pods that cannot be attacked, but they are really slow, a fast ship can outrun them and they have a limited range.
Ummm, hex map, and moons no longer occupy the same space as their planet, and the ship orders has had a revamp, you will need to learn how to program your ships again...
ooh, and the research/intel assignment has been modified, you cannot queue up research anymore and intelligence assignments are completely different...
Hex map, directional damage to ships, realtime combat with multiple ships on the same tile, many interface changes, 3d graphics, that's most of it.
Oh, and the screen where you balance your racial scores is gone, you just pick fixed values, no more trading individual points. All in all a lot of things were done that I don't really like, but there are some fun new aspects that are worth investigating...