I hated the lens flares too, they really irked me on my first viewing, because they gave me the s***s in Transformers too. When I saw it a second time my missus and a couple of our mates who came along for their second viewing had the s***s to, as they noticed every single one! :p
At Uni we found that the lens flare is good for two things in animation, for replicating light refracting off glass and metal surfaces to show off the surface, and to hide minor mistakes and modelling errors...