These are the things that seem most obvious to me, but I am sure there are others, given how annoying the issues I have in mind are to me. Please feel free to add your thoughts to all this, shoot my ideas down, whatever.
Moderation is anonymous
I say this is a Very Bad Thing. You can compare this to Kuro5hin, where you can easily see who did what to whom. Moderation with accountability allows anyone to see when a vendetta is being pursued, or when someone is systematically modding a subject down because they disagree, rather than because the issue is actually off-topic, a flame and so forth. I cannot begin to count the number of comments I have seen that have been modded down because they were contraversial, as opposed to offtopic, flamebait, or whatever else the down-mod claimed they were. The site's editors are also anonymous and that provides a hidden power structure which isn't a particularly good thing in any venue. I have read multiple claims that this poster or that poster cannot get mod points "because they modded something [a slashdot luminary] posted some time ago." If this is an illusion, exposing who did what to whom will in turn expose the illusion. If it is not an illusion, then exposing what happened should reduce the problem, because such action would rightfully be condemned by readers if it is inappropriate. I find the idea that the site's editors might be sneaking around and quietly muzzling moderators in a punitive manner more than a little disturbing.
So my first suggestion here is simply to lose moderation anonymity. My second is that if and when mod capability is removed from a user, the date of, and reason for, that action be posted right in their user page.
Many - perhaps even most - down mods are punitive or inappropriate
I suggest that the meta-moderation process be adjusted to include the ability to flag down-mods as obviously inappropriate, and to remove moderation privileges from those who commit such down-mods, as well as the down-mods themselves.
Up-mods don't need metamoderation
I suggest the outright removal of metamoderation of up-mods; if someone considers something interesting (or whatever) positive characteristic, who are we to say that this isn't so? That's the moderator's take on the comment, and up-moderation is a (very limited) opportunity for a moderator to "uplift" the story to the rest of us based on that perception. Upmods aren't harmful the way down-mods are - quite the contrary - and it seems to me to be a complete waste of time to metamoderate upmods for that very reason.
With mod points so scarce (and I agree they should be) we are forced to pick the things we really appreciate to up-mod. I rarely see an honest need to down-mod (obvious "first post" and gay/nigger trolls excepted), but I simply do not see a need to counter an up-mod. Someone thinks this, that or the other thing is insightful or interesting or sexy or whatever? Ok, that's at least notable - and that is exactly what an up-moderated and hence higher point comment does, it becomes more notable - not more interesting, not more insightful, but more notable. It might not actually seem that the applied moderation is accurate to us on reading the modded comment, but it is interesting that so-and-so (or at least "someone", if moderator anonymity remains preserved) thought it was worthy of a mod point. Comments can argue the issue if a poster is so motivated, and that seems like plenty of recourse to me. We see this all the time anyway; why not simply make it the official means of argument with an upmod?
Metamoderation is a scarce resource - put it where it does the most good
The removal of up-mod metamoderation could allow multiple meta-moderation of down-mods so that a reasonable, multi-user consensus that a down-mod is innapropriate can be reached. It seems to me that it should not be a light thing to say that someone is abusing the moderation system; you want to be reasonably certain. A meta objection to a down mod should cause that down-mod to immediately rear its ugly little head in a bunch of other meta-moderation queues so that consensus can be reached - and then corrective action taken if the mod is widely deemed inappropriate. This last point is important: It is a real shame that reasonable posts are permanently lost to the default view because some moderator was being a twit.
Fix the comment point system
There are several things wrong with this area of the site. The first is simply exposure, like authorship of moderation. Anyone who looks at the summary of points in a profile and tries to figure out what happened to a heavily moderated comment in a story is doomed to failure. It's Byzantine at best, and opaque and threatening at worst. Expose it.
Next, The math behind up/down mods is bizarre, to say the least. At a minimum, fix it so it is linear; or if not, then at least expose each and every mod point and show what it did to the story (along with the inflicting member - again, see Kuro5hin for a nice example of how this should be done.) Of course, if only this is done, an outcry will probably arise to fix the math, for the obvious reasons.
Expand the moderation choices
I have also seen lots of very good suggestions for additional moderation reasons. I'd like to see the readership discuss that here and perhaps a poll be subsequently created to see which new moderations should actually be added.
Story submission is entirely in italics
How is one expected to visually check the HTML of a story if the story preview enforces italics for the entire body? Why not use dark blue on white, and let italics flow according to the story tags so we can actually see what we're writing? You know, that radical new concept, "WYSIWYG"?
Sign the Polls
Stories are signed so we know who to thank (or blame) for the story. Sign the polls too. As I write this, there is a poll up for "favorite writing instrument" and the poll fails to include "keyboard" as an option. Somebody should have some digital egg on their face for that one. Maybe accountability will result in better quality polls. One can hope, anyway!