While doing some play testing I came to a similar conclusion about the clueing for the themed entries. If I wanted to be more clear, I could've included something about holes in the clues, but I really liked the "ace of _" construction (with each word having a /e/ vowel to rhyme with ace of spades and sound like a card suit). I also think it could be easy to accidentally make them more cryptic which isn't what I was really going for. So, I made sure to make some of the downs that checked the clues pretty unambiguous.
I agree about the two-letter words. They made creative clueing hard and solving them is never much fun either. I didn't even think about doing bars, but that's a good idea.
For
1A, yeah I was a little iffy on using "on" but I think the allusion to estrogen would be lost if I tried something else. Maybe I'll just rotate the puzzle 90° next time!
As for BRITA, just part of "Britain"!
Overall, thank you very much for the feedback!