Ideally, there would be some kind of incentive to reduce the total number of active transactions. The recommended fee could be lower for transactions that combined lots of low value coins into high value coins.
Minimum fees based on the size of the transaction already mean that tiny coins have less value than larger coins.
Right now the default client enforces some limits on transaction fees, mostly to stop transaction spam. Over time, those will go away, and each network node and miner will be able to set their own rules for accepting and relaying transactions, which means that there will be a market of sorts for fees.
But, when there are a lot of transactions to process, the miners will evaluate them in the terms that make sense to them. That mostly means that they will want a high ratio of fee to work. Each input to a transaction involves a certain amount of work, so there is no possible way to provide incentives to miners for consolidation transactions.
So, while consolidation may be useful to other parts of the network, it will not be prioritized by the group capable of making it actually happen.