1. Making Fan-games
You've heard it before, you're hearing it again. Let it go, please. As a matter of fact, with the new site changes, now is an even worse time to begin working on an anime game because it won't even be featured. If it somehow manages to get really popular and IP holders feel like they're losing money, they can and will shut it down. With an original game, everything belongs to you. No one can tell you what to do with it. It will be featured on the front page of BYOND which generates more traffic. Original games will also be more appealing to people outside of BYOND. I don't think trailers of little people with Vegeta-hairstyles punching pbags is going to be very impressive. However, something like this will definitely spark people's interest.
2. Making Boring Login Systems
Believe it or not, people judge games the same way they judge people: in the first few moments. That means that if you don't make good first impressions on players, you're losing dozens and maybe even hundreds of people. Your title screen should look nothing like this:
It's something I made in about 30 seconds, yet it looks exactly like the title screens that are used in over half of the games on BYOND, specifically fan-games. Here is a person who is doing right ( click to enlarge ):

Neat graphics, animated background, the font matches the retro atmosphere of the game, simple instructions, and a smooth fade transition from title screen to game with sound. Perfecto.
Make your games look inviting and feel alive when the player first logs in. Have things moving, maybe some epic music, don't use generic words like "New, Load, Del". Presentation is important!
3. Not Advertising
Why is it that Silk Wizard is the only person I see organizing a promotion campaign for his game? There are several great games on BYOND - NEStalgia isn't the only one. Decadence and Casual Quest aren't going to promote themselves. You should be scrambling to get all your friends to get the game seen. Get it on Machinima, get it on every forum you can find. Send out emails. Make trailers. More people = more money. You wouldn't have subscription options on your game if you didn't want any, so get your game promoted so you can make some! The more quality games get noticed, the more potential developers we'll get and then BYOND will really start being able to compete with the competition.
4. Electing Wild Team Members
I like the Silk Games Staff. There are only about 4 or 5 guys, right? It's not a game where the developer is tossing out moderator positions left and right. Your game doesn't need 20 moderators unless it's bringing in hundreds of players. Seriously, if your average player count is like 10 or 20, there is no reason you should have 30 admins. It only creates more conflict between player and administration which means more problems for YOU to fix since you're the man in charge. Don't give someone admin because you know them in real life, or because you became friends with them on some WOTS rip. Give admin because the person is a responsible team member who can do a great job at maintaining the peace in your game.
5. Not Encouraging And Helping Others To Be Successful
I think a big problem with BYOND is that people aren't friends. Whether it's because they're jealous or just don't like each other, people that could do a lot to help choose not to. There are a lot of people that will be able to help out with the NEStalgia promotion campaign, but because they hold grudges and would rather see a game by Silk fail, they'll just sit back hoping it doesn't work out so they can laugh at him.
Helping NEStalgia doesn't just help Silk. It helps the entire website. NEStalgia traffic is also potential traffic for you and your games. It's also, like I previously mentioned, attractive to great game developers who haven't discovered BYOND yet.
So, if Silk or anyone is trying to get their game out there, whether you like the person or not, help out. Usually it's just something as simple as copy/pasting a link on a forum, or posting a video on your blog. If you don't, you're a hypocrite when you claim you want to see BYOND succeed.
6. Whining About The Site Changes
Fan-games and especially ripped games are being hidden which is something that should have happened years ago. As a matter of fact, it shouldn't even be allowed to be on the site period. You don't have a right to post your game on BYOND.com because this website doesn't belong to you. It's called a privilege. We don't need any more of your sob stories about how anime games brought in so much traffic to BYOND, or how the people in fan-games are some of the most amazing people you've ever met. No one cares. If you don't like the website, guess what? There is this thing called Google, and through Google searches, you can find tons of other websites to post your game on or you can even create your own website yourself for FREE. So if you choose to stay here, on a website no one is begging you to stay on, then don't complain.
Make a list now. Or is your blog banned or something?