I will not say you are wrong for feeling as you do, but may I present a different take? The only options are to make the villains more and more horrendous and to have less and less a point (until everyone is joker/carnage/sabretooth) or to show SOME good in them. as such makeing room for new bad guys.
Magneto is a great X leader. Mystique and Destiny can be given a chance (especially with rogue and night crawler) but we need new bad guys to replace them.