Here are MY answers to your questions:
1) On benchmarks for the resistances of materials. I asked this awhile back, but got no answer, which is fine, as SUPERS! is designed for the GM to make such calls. What I tend to do is not assign Resistances, so much, as Target Numbers that have to be beat with a roll. This is what I've been toying with:
Wood Wall = TN 6
Brick Wall = TN 9
Concrete Wall = TN 12
Reinforced Concrete Wall = 15
2) On Armors - it's not really that type of game. I'd say most ancient and conventional armors would be at 1D (leather/light chain) - 2D (plate/kevlar).
3) All characters have all Aptitudes at 1D. As Narrator, you can decide whether or not you are going to allow a roll at all. It's your call. So, all characters have Medicine at 1D. A Brain Surgery TN, however, is going to be much higher than 1D can make. As Narrator, you might not allow a character with pilot to even attempt to fly an alien fighter, but maybe you'd let him after an alien spent a little while explaining the controls.
4) I interpret the plant control to be 5 plants (not types). So - not five pieces of straw, but certainly 5 trees. Or one wall covered with vines, 3 trees, and a venus flytrap.
5) As for mimic, I assume it's a maximum of however many dice you put in the power. The GM would have to adjudicate the yield of different substances. I'd recommend something in the vicinity of 2D for Wood, 3D for Brick, 4D - 5D for concrete, 6D - 7D for steel, etc.
6) I'm cool with the damage that Super Strength does. It's relatively consistent with other Supers games that I play. A character with a 30 STR in Champions, for example, does 6d6 and can lift a car over his head. A character with a 15 STR in Champions and an offensive strike does 7d6 of damage (but can only lift the equivalent of two men over his head). Some one like Spider-Man would be doing 4D damage from Super Strength. That's already better than someone with Fighting 5D can do, because Aptitude rolls cap at 18, no matter what. Low levels of Super Strength can still be useful (for lifting, or for Attack/Defense, if you've already blown your Fighting for either purpose earlier in the round).
Hope this helps!