That's a possibility, though there's a long history of transit users prefering through routes rather than transfers. If Muni could maintain 4 minute headways (or shorter), consistently, in the subway, that might be an option. It would reduce the wait times inbound on the subway to an average of 2 minutes, which is tolerable.

You still end up with the service irregularities on the surface sections, unless those rights of way are dedicated. Something which really should have happened long ago on Geary and Irving/Judah, 3rd St., etc. Maybe with the dedicated transit route on Market the idea will spread.

Extending the subway further out is another option, though expensive and fairly unlikely.