Gosh, reading your post made me feel so sad for so many reasons. You need to stop giving yourself a hard time and learn to like yourself and how you look. I suspect you're not ugly at all.
Why do you want to hide your freckles? They're beautiful. I used to work with someone who covered hers with thick make-up which rather looked like a mask and gave her something of a blank complexion. It rather drew attention to the fact she was trying to conceal her freckles. For the record, I have loads of freckles, never once have I ever considered hiding them and don't wear foundation or any kind of complexion correcting make-up. Instead, I have always concentrated on skincare so my skin glows.
As for your nose, well, I have an aquiline nose and again, never thought about trying to disguise because on a practical note, short of having an nose job, nothing will make it smaller. (And that has never been a consideration). Am sure some will recommend contouring but I think it looks ridiculous and can draw more attention. What I will suggest is that a centre parting is not your friend in this instance and an off-centre or side parting is best. Weirdly, wearing my hair pulled back from my face makes my nose look better too.
Lastly, thin lips. I am also thin of lip. In fact, my bottom lip is wonky and when I smile, I have a smile similar to Cherie Blair, so not good at all. I tend to stick to a good natural lip gloss and line my lips with a liner the same shade as my lips. I sometimes wear a blue-red lipstick too. Thin lips are perfectly fine and nothing to be down about. Would rather have them than over-inflated filler-filled lips.
Can't comment on the flat chest other than I would kill for that - clothes, particularly blouses and shirts hang so much better on a small bosom.