The limit is actually there to limit the size of a block. It has nothing to do with transaction fees. Click the link I posted: https://en.bitcoin.it/wiki/Scalability#Current_bottlenecks
It used to be 250K and then this year was raised to 1M so it probably will get lifted again. That is the goal of the project, to allow it to scale to at least PayPal numbers (46 transfers per second).