Doomtrain lets you edit default GFs abilities via kernel.bin edit
I discovered that, and spent some time last night and this morning learning about FF8 kernel editting. That does seem to be a good way to do it, however I did encounter one issue: you can only apply 21 skills to a GF, including the basic commands of Magic, Draw, GF, and Item. However, I found a way to do so;
I took 3 Gf's, Diablos, Cerberus, and Leviathan (based on Squall's base compatibility.) Then I separated abilities between the three, putting only the base four abilities on one GF. Then, in the save editor, I set them all to level 1, activate those three, and immediately junction them to Squall before I even enter the overworld. Then I set what I want to learn on each GF, based on how I want to build Squall. He starts with nothing, but after a while, he'll have a pretty decent arsenal of abilities.
To be honest I kind of hoped that I could put them all on one GF, and make it so you'd actually have to sit down and fight to earn the ability to junction to a stat or to gain a boost in strength. I also only had time to really include things that affect Squall, and did not include any abilities that affect GF HP or damage. It adds a new way to play without Squall himself relying on GF summons, and that's kind of what I wanted for personal story purposes; Squall doesn't need a GF becuase he learns these skills himself.
I am probably going to end up editing the kernel some more, maybe change those three GF's to be named after aspects of Squall, and even have maybe altered versions of his portrait. I'm not sure.
But if people are interested in this playstyle, I'll package this and release it as a mod.