I really enjoyed playing this. I played through 2 battles so far, but here are my thoughts (numbers correlate to your question list):
1. I think it's big enough. It allows for different battle backgrounds which would be fun.
2. It took me a moment to understand that Reputation was a currency and how much an upgrade cost was even though the amount was right there in my face. I would create a small icon that represents Reputation next to the amount they have to spend and next to the amount of the cost, just so the two numbers tie together visually.
3. I did at first because it wasn't clear that physical damage was happening. I like seeing the incremental health deplete in a health bar or % score, but that's just my preference.
4. I didn't pay much attention to the text...
5. The gameplay was fun. Once the balancing is done, I'm guessing will help too. I'm not a huge fan of having to wait for power meters, but maybe you could add a button to tap/click that helps block lasers or brace for a ramming attack? Just something to add a little strategy during battles.
6. The color palette, maybe? It depends on what you're going for...
7. Nothing more than I've stated already.
Once again, nice work!