You may want to consider AB Watley
http://www.abwatley.com
They have two or three different kinds of accounts, their basic Watley Trader, will allow you to trade 5000 shares for $9.95 - no additional charge for partial fills (even over multiple market days)
I don't personally use Watley, I looked into their fee structure for a penny trader friend who trades 5000 share and larger blocks.
He used Datek until they sold out.
His beef with his resulting Ameritrade account was ... he often trades low volume and it often takes two or three days to get a limit order filed.
Ameritrade would not charge for partial fills on the same market day, however they would charge for partials that carried over to another market day.
AB Watley says you can have partial fills carry over to an unlimited # of days without an extra charge.
Others have told me they can't get replies from Freetrade, which since they are owned by Ameritrade, you'd think there would be basic email support. There website makes it real clear that their business model requires they set limits, but the stories I hear don't make good business sense. -Maybe they will improve in time. I think the only hope they have is the Ameritrade name, that does make people think they are for real.-
There may be better soloutions but Watley seems to be worth checking out.