- re. multiple identities. cross-Signatures in the web of trust are done on individual identities, not the master key! So if you sign an identity and the key owner then creates another, that new identity will not carry your signature.
- re. key parties: so far it wasn't an issue because it was implicitly assumed that people attending a key parting were savvy enough to understand how to sign. For PGP to be democratized the concept of key party needs to evolve. I personally combine them with a small lecture on PGP use, and say "you get to sign each other only if you have attended the lecture including its small practical".
- re. software keys. These are typically considered as an extension to the developers' keys. You as a user shouldn't sign those.