You got my opinion on the html editor stuff The way it was coded made good sense in 1.9 (it meant there were literally no server requests when triggering the editor) but makes a lot less sense in 2.0 with the file manager stuff, so I think iframe would be preferable. (There may still be some difficulties in getting the editor - or more accurately, the e.g. reply form which includes the editor - 'on its own' in the iframe without a border and stuff, and to do with resizing the editor, though, so it won't be a walk in the park.)
Regarding the other ones:
1 System level flags - I'm not particularly happy with how this works - one goal which they do I believe achieve and I think is important, is that it should be possible to fix the options at system level so that they don't appear on each forum, making the forum settings form simpler. However there is a question as to whether you should EVER have that option on individual forum (see next).
1b RELATED NOTE - I'm also not happy with the 'limit on number of items' format for RSS/Atom feed items in forum (which was taken from standard forum originally) - I think this should (a) use a date as well, so it can be e.g. 'last 10 items or the last 24 hours of posts, whichever is more', and (b) not be a configurable option at all even in admin settings, it should just be fixed to something reasonable (like what I just said).
2 Yes there is global setting (which I implemented), these should be removed.
3 Probably, I can't remember what it does
4 This feature is important for us (without it we cannot offer open-to-the-public forums unless there is a paid moderator for each one, which is impractical), but I don't like the way it's currently implemented in forum as it's possible you may want to use that feature in other activities (in fact I think we do want to do that, at some point). We were considering making a local plugin, but it could also be a core subsystem. Note: you could implement it as a block independent from activities like forum, but for reporting, it's rather helpful to indicate which post you have a problem with, so we didn't think that was a good solution.
5 Yes the BCC feature should be deleted. It probably doesn't work any more anyhow. I think over half of the processing time is spent generating messages rather than waiting for the mailserver, anyhow. But, to note, I think to be 'Moodle 2-y' it should use the horrid notifications system instead.
5.1 I don't think we currently support headers in email but we definitely should at some point, this is a feature request we already have here.