The blocks that are ultimately submitted are the same, the change is in the way the pool and the mining software communicate.
Stratum pools basically sends a "block template" to the miner.
Quote from the BIP 022 Wikki: https://en.bitcoin.it/wiki/BIP_0022
This allows more of the actual work to be done by the miners instead of the pool. As hash rates increase, especially in the coming days of ASIC's, both network traffic and the work required by pool servers using LP will be astronomical.
In the realm of alt-coins, not as large of an issue for now, but it is still nice to use stratum. One will not see as large of a gain as with BTC, but still every little percentage of efficiency helps.