The L series Kubotas all use basically the same basic 3 range gearbox setup. They are all notchy and hard to shift when new. The other posters gave good suggestions.
1. Keep the tractor clean. Dirt and grit tend to accumulate under the platform, binding up the gearshift and other linkages even more. I used air or water to remove the crud as often as necessary to keep it clean, followed by doses of WD40, penetrating oil or other stuff to lube and protect the linkages.
2. The gearbox will probably always be notchy. It probably wasn't intended that operators would be shifting all the time. But giving the shifter plenty of use will loosen it up a bit, and the practice will let you master a bit of "technique" for shifting... how to position the tractor so the straight cut gears are not in tension, for example... something that I can't verbally explain. You have to get a feel for it from practice.
Keep the linkages clean, work them a lot and don't give up on yourself or the tractor!