Yes the thing about bitcoin is that inputs have to be signed individually even if they are all from the same address. This may change in the future if they manage to introduce shnorr signatures.
It shouldn't change. The current system is perfect we just need more intelligent policy for small input so users aren't technically forced to abandon currency.. Better distribution of the blockchain too using compression and torrents or something distributed with compression. LZMA2 solid compression or go hardcore with a PAQ algorithm.
BTW a better way to explain it is a payer address is a single input. All change addresses and destination address are outputs that don't get blockchain verification without a certain amount of satoshi to bytes.