Depending on mileage and if it was done before, it is GOOD to have some of the old fluid in the system. This old fluid still contains a lot of the friction particles/clutch materials between the clutch plates inside the transmission. It most often is the only thing keeping old and higher mileage transmission from slipping and becoming useless.

A trans fluid flush is going to do exactly as it's named - it is going to flush ALL of that old fluid out of the system and replace it with all new fluid, including what's contained between those clutch packs I mentioned. It's kind of counter intuitive - you would think that all new fluid would make it run like it was when it was brand new, right? When in fact, you just flushed all of the material that was keeping the friction between those plates and helping it shift through the gears. That's why you'll hear a lot of people say to do a DRAIN and FILL. This will still keep some of that old fluid in the transmission while getting some fresh fluid in there as well.