Compare the traditional block chain to an account tree:
A) Lets assume we have an account tree where each account consists of a public key & balance and a some other relevant accounting totaling 200 bytes per account.
B) Lets also assume that the goal is for this to scale to 100 million users world wide and that each user has exactly one account. This is not viable from a privacy perspective, so you would have to assume 10 accounts per user that rotate over time.
C) The resulting database size would be 200 GB without any indexes or other data structures.
D) To create a sha256 merkle tree on these accounts would require 64 GB
E) Assume you keep 1 month of transactions on hand for the mini-chain: 10 GB
Conclusion: The account-tree chain would require ~300 GB of storage and each user would still be limited to about 2 transactions per month.
The main thing that you are not taking into consideration is the fact that we wont reach 1 billion accounts in the account tree for an extremely long time, and by then it wont be unreasonable to expect people to deal with those sorts of large data sets (presumably). Now calculate how long it would take for the bitcoin blockchain to reach 300GB at the current rate of growth. Not too long I'm willing to bet, even with good pruning.
Furthermore, each account will be much smaller than 200 bytes, it will be closer to the 54 byte example you gave on the last page. No higher than 80 bytes in the worste case. If we assume 60 bytes instead of 200 bytes per account you'll find that it's only 55 gigabytes required. Also, the mini-blockchain will probably keep 1 weeks history or less, a full month is far too long if we need to account for very large transaction rates.
EDIT: But I do agree the system is not perfect and has its limitations, like any decentralized system. The answer is multiple competing crypto-currencies as you mentioned in your last post. But I don't think we would need thousands or even hundreds of coins, if we were to use the mini-blockchain / account tree scheme for those crypto-currencies, a few dozen or so could handle the entire worlds transaction needs I believe.