I'm surprised to see FFXIV not getting much in the way of votes. With the resilience that Warp threats have against mundane arms, I would think more people would be for picking a setting that would grant large swathes of the population magic, and the ability to wound denizens of the warp.
Servants and Guardians are great and all, but the former is distinctly finite in number and unless new Ghosts are going to be periodically made, guardians will be a slowly diminishing resource. At least Servants can come back if defeated, once true death sets in for a Guardian they're gone forever.
Add on the fact that there's only a so many thousands of guardians and that was to defend one city, they're going to be quickly stretched thin to defend a polity that spans multiple worlds let alone one that is adding more over time.
Guardians can't be created by anyone but the Traveler and their abilities are innate to them and cannot be taught to non-guardians humans. This is in contrast to Final Fantasy magic.
Plus, there's the utility of FF magic. Many sci-fi settings have teleporters but how many let a person go to a location from anywhere on a planet without any additional equipment save for a shard of magically attuned crystal at the destination? Final Fantasy magic has so many more uses beyond hitting harder.
Then you have fantastical magical items like the famous Phoenix Down, capable of restoring immense wounds.
Hrmm...you know, the more I think about it, the more the Planar Seed idea seems it might be more hassle than its worth.
There are other ways to balance things. For example you could make it a downside of going with Destiny and Chaldea, which bring with them entities on par with named Daemons, that Chaos will treat the coalition as a mortal threat and focus heavily on combating it while stuff like FFXIV and Nier are better able to fly under the radar.
FTL speeds can be nerfed or countered in a variety of ways. The more exotic systems may have trouble punching through in certain areas of space. Maybe Warp Storms mess with the fabric reality enough that ships cannot go to or leave FTL in regions with them, or if there is enough intense Warp activity it is able to disrupt the extra-dimensional spaces and make travel through Warp addled parts of space slow or dangerous.
Star Trek Warp drives do not function in places where Omega particles have detonated and destroyed subspace. You could have it such that there are swathes of space that have been damaged by exotic weapons dating back to the War in Heaven or the Dark Age of Technology that cannot accommodate other forms of FTL travel because of lasting environmental damage.
Halo's slipspace travel and Star War hyperspace are two methods of FTL whose speeds are dependent on galactic topography. The former already features instances where planets close to each other in realspace have longer travel times than those that are physically further away because of that. You could have it so that 40K's galaxy is structured in such a way that quick routes don't exist or make it so that the Coalition has to put in significant effort to chart them out.
You could also leave threats in FTL, such as the Beast from
Homeworld: Catalyst, which existed in that expansion's particular interpretation of Hyperspace.