If you decide to use ECLs for creatures in order to adjucate it, then Shapechange would become one of the most useless spells in existence. Anything actually worth using a 9th level spell to turn into is going to have a massive ECL (for example, a juvenile dragon, which wouldn't even be good enough to use as a form in epic levels, would easily have an ECL of 25+).
I'm not a fan of the "the DM is always right" philosophy.
If you're an epic wizard with shapechange, you should easily be able to pull off a 50+ AC; epic DR is just another insult piled on top of that, and really won't matter -- if whatever the heck your fighting can hit a 50+ AC, then it can handle epic DR.
But Shapechange actually grants Su abilities now? I can see why your DM is freaking out over the spell, if that's the case. WotC is down, so I can't check the SRD.
My group's always handled familiarity as "if you've actually seen it in action, then you're familiar enough for the spell to work."