I really do prefer Logan suffering amnesia from the procedure. It makes more sense, and in the X2 flashbacks, you hear voices say "He'll have no memory".
Plus, Stryker's whole "I can make this all go away" speech from the trailers heavily implies the procedure will make his memories go away.
I would prefer Logan to volunteer for the procedure to make his memories all go away (the pain of losing his love, Silver Fox), and starts working for Stryker after the procedure. But certain truths become apparent to Logan, pieces get put back together, and he rebels against Stryker, frees the captive mutants, etc...