It would work as follows, and NO I haven't really thought this through it's just an idea!
Imagine it was 2009 and there was a small number of 250 BTC in 'Batch 1', once the number of BTC needed to go above 250 BTC two new Batches would be created each one with it's own Merkel Tree until 750 BTC and so on. Eventually there would be a large number of trees, allowing small scale pool miners to dominate a single or small number of the trees and their block chains.
This would also create a potential partial payment problem, where you send 3 BTC but only receive 2 BTC since 1 BTC ends up on a bad block and needs to be resent.
Since most of the BTC currency supply is already available it's a bit late for BitCoin, but could be used for new crypto currencies.
Any thoughts on this idea?
Cheers,
Scott