Two Towers
Obviously this is a subjective question, however having played both and had to choose which one to review for publication I heartily recommend the Two Towers game. It is not only fun to play and drop dead gorgeous, I think it keeps the game simple and captures the spirit of adventure and peril of the story..
Fellowship has some glaring problems, no matter the platform. I think it was rushed by the developer to compete with Two towers and capitalize on the movies. Sierra has had the LoTR book conversion rights for quite a few years and this is the first product they have actually turned out..