well there is only so much you can do with this mesh and unwrap. In general, as said before, the straighter your uvs the cleaner this will be. if a line goes horizontally or vertically it will be cleaner as if it goes diagonally. Thats almost independent of resolution and antialiasing. Of course the more blurred a line is, the less visible it will be, so you can try to crank up the sampling of the bake, this should definitely help to disguise the issue.
It's a resolution issue, you could try to use a larger softer brush, or higher resolution textures, or try to align the UVs so that the panel lines are mostly vertical and horizontal on the UV.
Do you notice the bubbling when viewing the entire mesh? It's possible you are too zoomed in and focusing an issue that no one would ever notice.
Yeah it's only visible when really closely zoomed in, but still, I wish there were a way to make it look better. Doesn't even need to be with textures.
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While the actual detail issue is here:
Would I look for anti-aliasing in Substance Painter or what? Is there a better way to get those panel lines in?
Do you notice the bubbling when viewing the entire mesh? It's possible you are too zoomed in and focusing an issue that no one would ever notice.
http://polycount.com/discussion/155894/decal-technique-from-star-citizen
http://wiki.polycount.com/wiki/Decal