If I'm understanding well, what he proposes is for the chain to maintain a ledger with pairs (address, total balance) and transactions just saying "substract X from account Y and add them to Z" instead of "spend everything in Y, X in Z and the rest back to Y". Very similar to Ripple's ledger.
This would be a huge refactor and a hardfork, but I haven't actually heard any argument or explanation why the system isn't like that from the beginning.
I'd be interested to know that as well.
Traditionally, currency systems were designed the way OP suggests. Not sure what was the rationale for designing the transactions this way. It's certainly irregular, but perhaps there was some kind of articulated reason somewhere.
It's certainly possible to have a TX format as OP suggests. Not sure how you could implement complex transaction types ie. Contracts though. It is true that it would far more efficient as far as computing balances go.