For container-grown trees, you have the benefit of having a nice plant to drop in the ground whenever you want. Nowadays, most professional growers cater to this market. Bare-root trees can only be planted in early Spring, and the idea is often intimidating to novice gardeners.
Because of the disruption caused by bare-rooting a tree, you may initially see slower growth versus its container counterpart; however, I've also seen the opposite. I had a bare root bald cypress put on two feet of growth this year.
However, in my experience, container-grown trees pretty reliably have many problems: poor media, circling roots, girdling roots, the tree is planted too deep, etc. Nurseries want to produce pretty specimens that get bought up at retail nurseries. They do this on a large scale, so many of the little details that ensure the overall long-term health of the tree are sacrificed for the sake of money and time.
Additionally, container grown trees requires "foreign" soil to acclimate with native soil. This can slow down establishment.
All things equal, I'd choose a bare root tree over a container tree; however, many species are simply not available bare root, so container-grown may be your only option. There are root treatments you can apply but these are generally not required. Because the root system is small, you'll have to ensure adequate water for at least the first year of growth (also true of container trees).