I've had the same history with the series as the OP, except I don't think I've ever played hotseat. Still, I think not having it is stupid.
Some people obviously like it, it's a natural thing to have, and there's no reason not to have it.
The implementation of it ought to be close to trivial: save game, edit save file to change which player is playable, load save file - just add a screen off the main game menu to set it up. You could probably even write a script that does it manually even if it's not in the game, as long as the save file isn't encrypted. Hell, I wrote my own 4X game for fun a few years back (in python of all stupid decisions I've made), never finished it, but I still had a hot-seat game mode in it. It's that easy to do.