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The only example I can think of is Supreme Commander (and presumably, by extension, Total Annihilation, which I haven't played yet). The ships handle how they should, and the scale is large enough to allow for that. The variety of ships is good, the factional differences made it interesting, a lot of thought went into their capabilities and armaments, and there's a good balance of simluating real-life warships to spicing them up with sci-fi ideas. What else should I play if I enjoyed that?

Fall of the Samurai.

Shogun 2 ships were pretty impressive. There were different types of crew members who apparently did different things. Unfortunately CA doesn't understand that fleets should have faster movespeed than land armies, so there wasn't much need to have naval battles in Shogun 2. Rome 2 was a major step backwards as naval battles were greatly simplified.

S2/FotS built on Empire, naval combat wise, but they kept the rock paper scissors formula (which was fine there) and dumbed everything else down too. S2 was simplified, but its mechanics worked better than Empire's. Now CA have been a garbage developer jizzing fan-service for a decade and there is no competition.

We'll never get a good Empire 2 because of anti-colonial butthurt.

Its the anti-colonial butthurt that kills all hope of Empire 2 forever, but we were never realistically getting another good TW from the creators of Rome 2, Warhammer, Three Kingdoms, and Pharaoh. Cuckrative Assembly suck at the niche they created out of nothing.

Some indie really needs to make a new colonial era strategy game, they can cash in on telling jurnos where to stick it.