Well let's be fair, Napolean was an expansion pack. Empire: Total War is the original. And the Total War series has been very successful as a whole.
Back on the subject now.
Only ones I have played is Sins and Star Wars Empire at War(not the greatest example but still valid to bring up (never had the money to go crazy with video games and minis at the same time
)). Sins doesn't have much of a 3-D effect to it and having played it extensively I would say its more of a 2-D game with 3-D graphics. But something I think for a BFG game is the whole game may not be suitable for RTS consistently like Sins. It's entirely doable, but I don't think it works well for it. The appeal for Battlefleet Gothic is to focus more on the tactics of each battle, not the grand strategic level where you just build a fleet and send it off and hope it's enough to conquer the system without needing to dictate every ships maneuver.
Now I honestly think a 40k Universe BFG space game is not hard even for total 3-D. I think the fleet with the hardest time in this situation is Chaos. Without a lot of firepower to the front and no hardened armor, it seems to me they will always play more stand-off ish. Imperial wouldn't even have a problem. Go straight at the enemy and rotate the vessel if the enemy chooses to go above/below the area of engagement. I could see ramming being an issue though... Otherwise, the alien fleets will play a lot like most of the fleets that exist in games now (such as Eve).
-Zhukov