The idea that, almost romantically, a body and neck are made 'together', is funny at best and ridiculous at worst. There's absolutely nothing 'wrong' with a Warmoth as a guitar. It's a great blank sleight for you to work your own magic on, like nuts, fret ends, fretboard rolling, etcetera. Warmoth gives you the parts to success, you just gotta make it a success by yourself, and that takes a very long time.
"great", means a certain level of consistency. It means that all your fret ends look the same, aren't sharp, and are the same guitar to guitar. It means that a guitar goes together almost like an ikea piece. That you only need a dremel to polish the frets. That you don't need to constantly go back with superglue, lacquer plane, and sand paper to smooth out chips in the finish, because you forgot to ream a hole or two.
"Great" means, no gaps between the neck and body, fretwork that's even all across the board, a fretboard that's so level that when you press in the frets and check with a fret rocker, you can level the frets with grit 600 instead of 220 or 320 because you're just doing a check instead of leveling for real. "Great" means a neck without dead spots, consistently between guitars as well, a guitar that has turned out exactly as intended where any pickup will make the guitar sound like a billion bucks and you don't need to swap a million times to find "just" the right pickup.
And almost all of that is just a story on paper. Look at this LP and telecaster. I made that LP in 2015, the tele in 2020. The differences are stark. The Tele is finished better. Fretwork is more precise, the inlay is well.. there (The LP has no inlay!). The neck angle worked out exactly as planned, the neck sits above the top of the guitar just right, the finish is exactly as it has to be. Yet... It took a few pickup sets in order to get this guitar right.
But that LP. When I made that LP, I drilled a hole too deep in the neck when I lined up the fretboard's pilot hole, so now there's a tiny hole in the neck. I mucked up the headstock shape, neck angle, pickup locations, I drilled straight through the top when I was recessing the inside of the switch cavity.
Yet. The LP sounds and feels unlike anything I've ever made. It sounds perfect. I wacked in this pickup set and BOOM. This was IT. This as it and I never, ever, looked back. Not a single hair on my body would contemplate to swap pickups here, whereas the tele is still open for swapping.
My point is that 'great' is so extremely subjective and cannot be determined. Specs only tell part of the story. I do know one thing for sure, though.
If a guitar fights you, if you're struggling to make it work from the start, it will be a fight until the end. So those guitars simply won't work as well as others.
For example, that last one. It was a fight to get the neck right. The finishing was a nightmare. Eventually, I swapped out the bridge, pickups, bindings all over, and a new color. And still, the guitar fought me. Sometimes you have to say: it's enough, it's over. Ironically, I'm the only one who feels this way because all who tried it, adore the guitar.
So, what makes a great guitar? Just basic build quality? No. it's the sum of its parts.