I would accuse blockchain.info for the problem. I might be wrong but before they decide to make their new wallet(last year) that was forcing everyone to use 1000000s of different wallet address...
It seems like you don't have a full understanding of how addresses are used. Using multiple addresses has absolutely no impact on Bitcoin's performance or throughput.
I'd agree with you, however how blockchain made it is when you send 1BTC but have 500 btc in your wallet, you are making a 500 btc transaction. it move 499 btc to a new wallet, and 1 btc to the destination wallet.
The wallet which sent the 1BTC end up with 0 BTC while a new wallet have all balance.
I am pretty sure 1+ million people sending high amount of bitcoin at some point will make difference.