In K9:
1) There's an option for multiselect boxes. They checkboxes are on the left, though.
2) I like that feature. You can mess with the font sizes, but I don't think you can turn it off.
3) Just choose the dark theme.
But forget all that, the stock email client is scary to use. Check out my post here:
email alerts
It's sendin' out random emails to people, not polling, sending out gibberish.
Plus, K9 has more features. Different notifications light colors and sounds per account, ability to copy the text of an email, search, ability to choose different From addresses, etc.
I believe that K9 is open source and I think the devs work for Google and it's part of their 20% project. Don't quote me on this, it's just that their google code site says that they plan to fold K9's features into the stock client.
Maildroid is another one, but I doubt it's open source and who knows who makes it.