The protocol whitelist is disastrous in my opinion. If at all possible that particular part should be dropped.
My top priority for this topic: Whatever comes of out the auto-linking discussion, there must be an explicit way to generate links to an arbitrary URI. Beyond the inherent absurdity of a text format being aware that spotify and secondlife exist, artificially limiting future protocols would be, in my opinion, very short-sighted.
Burt’s most recent proposal seems to address my concerns handily.