RE: 80% versus 90% :  I think a default of 80% will get us a lot of "the fee estimation logic is broken, I want my transactions to confirm quick and a lot of them aren't confirming for 2 or 3 blocks."

RE: RPC argument:  I'm reluctant to give too many 'knobs' for the RPC interface. I think the default percentage makes sense as a command-line/bitcoin.conf option; I can imagine services that want to save on fees running with -estimatefeethreshold=0.5  (or -estimatefeethreshold=0.95 if as-fast-as-possible confirmations are needed). Setting both the number of confirmations and the estimation threshold on a transaction-by-transaction basis seems like overkill to me.