I think this problem would need to be tackled on several levels to be effective.
CEO: We should want and have a CEO that is not only interested in the business side of reddit, but should also be active in the community. Seriously our current CEO has no idea why reddit is the way it is and what the userbase wants, she is completely out of touch, and doesn't realize that reddit is not just a static product to sell to advertisers. The size community is what makes reddit so valuable not the advertising space, and if you don't treat the community well it will shrink and reddit will lose value. Having a CEO that cared about reddit and had any long term business sense would eventually cascade into fixing most of the issues.
Admins: Need to be more active and more responsive when shits happening, see the /r/technology fiasco earlier this year. The admins did nothing for a very long time while a few power users used the sub as a karma factory and censored a huge portion of the posts just based on buzzwords. Really in general need to be unbiased and responsive to issues raised by the reddit community.
Mods:I've seen a lot of mods in different subreddits just power trip or be general assholes just because they're mods. So for this i would say too all the mods who rule their sub with an iron fist, stretch rules to delete posts, censor their sub ban for no reason, get your head out of your ass, you aren't the next coming of jesus. You're a janitor for an internet forum. I would say though that in general the mods on subs i frequent are really good, theres just one or two that really piss me off.
The site itself: As others have mentioned, making RES features built in, better search function, better mobile site are the big ones.
The Users: Stop thinking that your opinion is automatically right and that you are super smart. The site is full of pseudo intellectuals that think they are geniuses and everyone with a different opinion is wrong and stupid. This can't really be fixed though