Many people keep seedlings in pots that are 4-6 inches for the first few years. This is because it is easier to promote better surface root growth using a shallower pot vs. growing in the ground and also for easy in root pruning. Growing in the ground often comes later after good radial roots have started to grow in the pot and now need to thicken along with the trunk.
Trees that are left growing in the ground when young ofter have one or a few very strong roots as opposed to the thick full nebari we want in finished bonsai. Growing in pots helps control roots in the earlier stages which makes for a better finished product. Correcting poor rootage can be done later, but is difficult and time consuming.
But while the tree is in the ground, you should just chop down to get taper and movement.
http://www.evergreengardenworks.com/articles.htm has some helpful articles on japanese maples and getting taper
The simple answer as to when you should repot the tree is that you should do this when the tree achieved the trunk thickness desired in the final tree. So that like 2 inches in a shohin, 3-4 in medium size trees, and 5+ in larger size trees