Responses are based on MozMail, but might help you out:

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1) I still can't believe they went through till this release with this annoying system of forcing a new set of folders for every email address you own.

Also annoying. Switching back and forth between Mac Mail and the PC just makes this painfully obvious.

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Why can't I have something that will check them all at once?

Yes. Infuriating. In Moz, there is a pulldown on Get Msgs that lets you choose Get All, but that should be the default, not the exception. If you setup your accounts as autodownload, obviously this isn't as big of a deal, but i definitely obsessive-compulsively want to check them all again.

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2) there doesn't seem to be a way to make the default screen anything other than the stupid welcome screen. Why can't I go straight to the inbox?

In Mozilla: Edit=>Preferences=>Mail & Newsgroupss=>There's a checkbox labelled "When mail starts show the Start Page in the message area" that can be turned off. Not sure if this is the same for Thunderbird.

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I'd love to be able to set the program so that when I reply to someone, the cursor is automatically placed at the top instead of the bottom.

YES! Why this isn't the default -- no idea .. So this is in a really weird place in Moz -- it's a per-account setting. So Edit=>Mail & Newsgroup Account Settings=>under each account=>Composition & Addressing=>pulldown menu with "start my reply above the quote"

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when I double click on a folder to expand it, it instead opens another instance of Thunderbird.

Yeah there are a lot of these annoying things ... For instance, File=>Exit on MozMail exits all browsers. Yeah, thanks Mozilla, because that's certainly what I intended. I don't care that it's a single process, that's a dork attribute -- they're clearly separate contexts to an enduser.

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the spam filter does not work

I actually just started using this and it's been OK for me so far, but it's too soon to tell.