http://world.std.com/~dtd/sign_encrypt/sign_encrypt7.html
PGP and S/MIME do not encrypt the subject line of emails; this is an easy way to leak information. You also do not get encryption of References/In-Reply-To headers, and various other headers that can leak information.
You can't take a signed message that was encrypted with your public key, decrypt it, re-encrypt it with somebody elses public key, and expect it to still appear signed by the original sender when the new recipient decrypts it.
[edit] There are of course serious problems with the lack of header signing/encryption and replay attacks though I agree. Hence why I add a small note at the end of all of the pgp signed comments on my blog: "This signed text was written for https://grepular.com/ only"
Your points about subject lines and other assorted headers are correct.
I do agree with you that PGP and S/MIME would be awesome features but most people using Linux are so frustrated with default apps that I think they wanted to show their focus on the basic workflow.
I'm Linux user and don't feel frustrated. Am I missing out?
Secure email is not possible unless you're all being very careful, or you're using some other protocol.