What better options are there, if you're aware of these weaknesses i'm sure you're aware of better options.
More in keeping with the Unix philosophy of doing one thing and doing it well (GnuPG in particular does a mediocre job of many things), the best move is to replace it with a suite of single purpose tools.
For example, signing commits with minisign or signify.
>For example, signing commits with minisign or signify.
These tools don't work well with git or the git forges, and they do not work at all with fossil. (Obviously signify is a good choice if you're using OpenBSD.) Furthermore they lock you in entirely in their choice of algorithm, Ed25519, which may not be what you want (Why not Ed448?)
As far as adoption goes, and adoption is hard to get going, GnuPG is what is used in Linux the most...
"Github supports GnuPG signatures" does not contradict the statement "GnuPG is trash". I will not engage further, it's obvious you are not interested in honest discussion of the technical merits.
The issue is mostly with git itself, e.g. take a look at
git cat-file commit HEAD
tree <tree-hash>
parent <parent-hash>
author <author-name> <author-email> <timestamp>
committer <committer-name> <committer-email> <timestamp>
gpgsig -----BEGIN PGP SIGNATURE-----
<ascii-armored RFC9580 signature>
-----END PGP SIGNATURE-----
<commit message>
You can add a patch to git to support more signature types than just OpenPGP. You may then be able to move mountains and get GitHub/others to join in the validation. Finally, if you can find bugs/exploits in GnuPG, you should report them and you will definitely get credit and recognition for them. They are not trivial to find.