I'm getting better at the MU, won a tournament round against a good sub player last night.
I play heavy weapons - his machine guns go through the ice clone and hit sub, but you have to be really careful. Also his ground pound goes through the clone. Make sure you are full screen if you try to zone/ counter zone at all.
If clone is out, I try to stay right in my f21 range and outside of his low footsie range. I block high (I'm expecting his overhead, which I can punish or for sub to jump in, which I can anti air and full combo). Most sub's won't slide because it is so damn punishable. Sometime i'll walk up towards the clone and then back up a littlebit to try to get his normals to whiff and then I punish.
Getting cornered sucks. Try to save some meter for getting out of there, as it will inevitably happen. Otherwise, block, counterpoke, and reverse throw to switch positions. Maybe NJ1 every once in a while.
Just play patient. You can still rushdown, just play it a little more methodically (i.e. it's not worth poking with a d4 after a block string and hitting an ice clone)