I took mine in for this at the beginning of the month.
Dealer ordered a new transmission. Took 5 days to get the car back.

Now I have a brand new transmission (18k miles on the car) and I still feel it the notchy shifting.

 

When I'm driving normally and not "power" driving, I shift from 1st to 3rd most of the time and then from 3rd to 5th and if speed allows to 6th. Driving this way gives me buttery smooth shifts. I always use the appropriate gear for the way I'm driving...normal or aggressive. If I use all the gears when I accelerate that means I'm going for power. The shift into 2nd from 1st is a bit notchy, but the car really takes off from there.

I've done this with all my manual shift cars for decades and never had a tranny problem. Plus it helps improve gas mileage.

 

1) switching the OEM clutch fluid to synthetic aftermarket*** made clutch feel MUCH better. favorite thing I did. I did not expect it to make such a big difference. *got this tip from GM/corvette forum. they said oem fluids are usually junk.

2) screwed the clutch pedal alllll the way down so it engages like a normal car. I also lifted the rear wheels in the air. The wheels/transmission did not engage at all with the clutch adjusted like this and pushed all the way to the floor in first gear + engine reved to redline **got that test idea from dsm forum and ACT's website

3) screwed the brake pedal back so that its aligned with the gas pedal. got this tip from a lotus forum. much easier heel and toe (the elise fsm actually suggests to allign pedals for track use).

4) adjusted the accelerator position sensor. loosened the sensor, and with car on, pivoted it until I got an idle change, then backed off. Made accelerator pedal more sensitive. took some guts to do this because the FSM says "dont f%ck with this ****"

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car shifts like my old integra now.

the biggest problem i think was the OEM fluid and the delay in the gas pedal (the clutch engages where you want it, the gas pedal takes its sweet time)