When I say that a transaction is not a first-class citizen, I mean things like the fact that the question "I have this address, how many bitcoins do I have" is not really answerable; redeeming existing incoming transactions may rely on information outside of your key pair.
You're correct that as it stands, 1:1 transactions are pretty much all we have to deal with, so long as IsStandard doesn't change. The fact that the script language exists is worrisome, as is the fact that IsStandard only applies to relying of transactions by clients, not transactions in blocks.