Poor Moderation - Spam and usual brimstone stay up indefinitely without mass removal, moving to proper boards, etc. Bans are too light for big offenses. A QnA and guidebook would solve this, with accountability for mods and jannies. "Why didn't you move this post, dude? It is explicitly in the guidebook!" "Don't just remove the posts next time. Ban him if he keeps doing it."
Contrary to popular belief, rulecucking is not rules that are tough, concise, and fair. It is really about "hidden" rules and exceptions, which is quite the opposite.
Bad utilization of McCaptcha - NuDev kept tightening the screw until it was too harsh and intrusive. After that, he removed it from /soy/, allowing bots to rain free. The McChallenge also
sucks ass and swallows.
Downtime: Not a big problem in the past. For some reason, it is now. I have no idea why. When my devices have problems, I do the old plug-out-plug-in routine, and it's always resolved in less than 10 minutes. The simplest fix would be backup servers, but it requires monetary investment for a low payoff.