Yes, noticeably different although not necessarily to the point that some of the aftermarket sets take things.
Both RA & STi gearsets have larger teeth than the standard WRX gears. That may have changed for '06. I have not had a chance to check. But since the WRX is now coming with the 2.5L turbo its probably got the same gears as the Legacy 2.5GT model which are similar to the STi gearset.
The tooth pitch unfortunately is limited by the diameter of the gears and the ratio. If you look at a 6MT you will find they have increased the gear shaft centerline distance from 75mm to 85mm. This allowed them to increase the gear diameters and run a stronger tooth pitch.