I very much agree that Hotseat, LAN, and/or an email-esque play system is the way to go. But there should never be a time that other features should be sacrificed for these things. In fact, it's hard to see how there could be features sacrificed, especially considering these sorts of games just aren't for playing with random strangers, anyway. It's like getting together a bunch of friends to play Risk. People who should be expected to wait out turns, regardless of how long they take. And if they need to scale it down, then the game's natural features should be able to accomodate this, anyway. Like choosing smaller map sizes.
Civilization is what it is- I really don't see how Multiplayer really affected its development. Much as Master of Orion is what it is. Personally, I just don't see these styles of games lending themselves to scenario-oriented gameplay, anyway. It's always been about randomized worlds/galaxies and exploring, expanding, exploiting, and exterminating as you see fit on your quest to galactic dominance, with each game capable of very different experiences thanks to the random maps and rivals.
I won't argue that the campaign for GalCiv 2 was a waste; any decently-written campaign is enjoyable to experience... but at the same time, it seems out of place for a genre whose core design is all about players making their own mark on a unique galaxy or world.
Scenarios, similarly, can be fun, but in the end they're also one-shot experiences. Civilization also uses them to great effect, but they also add the best ones in expansions, like Beyond the Sword for Civ IV. AfterWorld, for instance, is an impressive piece of work that made a Tactical Squad-Level Strategy like X-COM out of a Civ game, playing completely differently from the vanilla Civ. However, I have also played Civ IV: Colonization, and although it was an interesting experience, it also felt like a cheap experience next to a proper game of Civ IV.
The true longevity of the 4X genre is the richness of a random game experience. Not scripted single-player events and encounters, and not dumbed-down multiplayer experiences. And just adding friends and family to the rich random game experience should be the core point of 4X multiplayer.