You're not missing anything - the Fighters Guild in Morrowind really is designed as the low-stakes path, and that's kind of the point. But I'd push back a little on dismissing it entirely.
The thing is, Morrowind's Great Houses are faction-locked. You pick one and you're basically committed. The Fighters Guild, Thieves Guild, Dark Brotherhood, Mages Guild - those exist partly so you're not forced into house politics if you don't want them. Some people just want to be a sellsword, and that's valid.
That said, if you want actual stakes, the Fighters Guild does get more interesting if you A) actually engage with the NPC dialogue and backstory (a lot of it is just sitting there in dialogue trees, not quest markers), and B) push far enough to hit some of the later guild rank quests. The early stuff is genuinely just "kill this guy" or "retrieve this thing," but there's a reason the guild's reputation in Morrowind is... complicated. Without spoiling it, the guild itself has problems that become apparent if you're paying attention.
But real talk: if your buddy is having more fun with House Redoran intrigue, you might just prefer that playstyle. Morrowind rewards deep engagement with whatever you choose. If you want to switch now, the houses are still available - you're not locked in. Some people do both on the same character, though it gets messy depending on which houses you join.
What kind of character are you playing? That might matter for whether the guild stuff clicks for you.