Maybe, I do admit that it had a different feel to it than the companions. Then again, I liked the kinda cultural influence you had in the Companions. They felt Nordic, while the fighters guild in Morrowind didn't feel Dunmer. But yeah it could be cool. I'm proabably more excited to get a closer look at the College of Whispers and the Synod.
And we don't know when and where the next game will be set. I figure the Thalmor will show up and screw everyone during the time in-between Skyrim and TES VI, that way they can make your descission in the civil war irrelevant.
So back on topic, I didn't miss the fighters guild, but it could be fun to see them again. I enjoy factions with cultural influence though, like the Companions and the Morag Tong or the Great Houses. So no matter what, I hope we will get a cultural faction, it doesn't have to replace the fighters guild though.