The reason that it is so "difficult" to get the PS1 Final Fantasy games remastered is either because they don't have the original, uncompressed painted backgrounds or the originals were made in a very low quality. In either case, they would have to be redone. With the more recent 3D games and assets, it is a bit easier to remaster because the textures (and in some cases, models) are created at a higher resolution or polygon count. When you remaster them, you actually use the existing higher quality assets.
The PS1 Final Fantasy games make (heavy) use of pre-rendered backgrounds. Basically, they use 3D assets, render them, take a picture, and put it into the game. This is why if you use an emulator and upscale everything, the backgrounds look extremely poor. You could (in theory) go through and re-create all the assets that were used to make the background and capture another picture at a higher resolution to use in a remaster, but that is obviously a lot of work. You could also go in and try to manually re-draw all the backgrounds, but that is also obviously a lot of work. There's no way to make an image bigger and add information to it (that is, if you just make an image bigger, it gets blurrier). There are techniques to guess at what the image would look like, but those generally look bad because there is no generic solution to do it. Different algorithms are better for different images and none of them will look as good as if you did it for real.
In the case of Xenogears, I think the opposite is true (based on a few screenshots and videos, as I've never played it). The background in the game appear to be polygonal real-time renders while the characters are sprite-based. I imagine that there's no way SE has those assets, though, as they didn't develop the game (Monolith, perhaps) and just own the IP.
EDIT: Here's a
NeoGAF link about Final Fantasy IX backgrounds that were included on the disc vs original concepts.