Lighten up on enforcing rules for the sake of enforcing rules. This is a problem all over StackExchange, and academia.SE is no exception.
Comment deletion is a good example. Newcomers may not remember that comments aren't for answers, and may think comments are for short responses. But their (possibly highly upvoted) comment may get deleted for no other reason than too many other comments accumulated below it, so a mod moved ALL the comments to chat. Which is the same as deleting them, for people who have no interest in using chat. A lot of thought goes into some comments, and nothing discourages new users more than semi-arbitrarily deleting the content they contributed. (In fact, I am not a new user, but I still struggle with this. Sometimes, the thing the OP most needs to hear is not a direct answer to their question, so it wouldn't fit as an answer. I have had such comments removed without even getting a notification, and it makes me want to contribute to the site less.) At the very least, there should be an upvote threshold above which comments aren't removed so willy-nilly. (Or maybe they can be automatically converted to answers in some situations?)
We should also not be such sticklers for whether something is on-topic. Blatantly off-topic questions should of course be removed, but there seems to be a culture of "when in doubt, say no" just because people like to be sticklers for rules. It's not hard to see how this discourages newcomers. If we're not sure, why not leave the question up and see if any good answers result.
We need something like "Rule 0" which would roughly state "ignore the rules when following them would make the site less useful." This would not only make the site more welcoming, it would make it better.
(The obvious response would be: if the rules are hindering us, we should make better rules and follow those. But life is not so simple. We know good content when we see it, but we can't always write down a finite set of rules that will reliably sort good content from bad.)