well, for one thing, the series author overlooked one fact: even though you can control your bones, i seriously doubt that you cold nullify the pain you would feel from your skin ripping. im quite shure it would be too painful to use very often. besides, the sharingan or byakugan could easily track the bone projectiles and allow the shinobi to dodge them. wearing the bone-weilder out would take some time, but is definitly possible. plus, i have no doubts that sasuke's chidori or kakashi's rakiri could easily penetrate the bones.
in my opinion, anything that gives you a really good tactical advantage would be better in a fight than something that just gives you really good defense and offense. plus, i actually thing the sharingan is the most advantageous, as it has two forms when most kekkei genkai have but one.