1. Too many things are paid
Usually, when servers get popular, the owners make things cost more and make them paid. Most things that you could get or do in a server for free, you have to pay for. Maybe you've seen this from your own experience, but it's really annoying. It makes people dislike the server, and the solution is simple. If you decide to make more money, and make things paid, make sure there's still a way people can get some of the paid stuff for free in the game by working really hard at it.

2. Portals and lobbies
I'll make this simple. If you have a lobby, it means you probably have multiple minigames and servers. Many good servers, have one game. Or one purpose. Such as, a capture the flag server. It's only capture the flag. If people are looking for capture the flag, they will try your server. If you have a minigame server with 50 games including capture the flag, people won't go on it. Because they want a server that specializes in capture the flag. Sometimes, minigame servers can be good too. But there seem to be too many of them. And they have a lot of the same games and lobbies. Come on people get creative! We need new types of servers.

3.  The bad crowd
People who use bad language, flirt, and hack are all part of the bad crowd. Let me explain. Your server attracts different types of people. Most servers do not specifically attract anyone, and because of that, the bad crowd joins, because it's just a normal server and they would like it just as much as anyone else. And the bad crowd is huge on Minecraft. If you want to get rid of those people, make your server so it doesn't attract that crowd. Make it attract other people. Make the minigames math-related. For example, green and red sheep that mean add and subtract and whoever can go the longest wins. You can get very creative with it. But if you really don't want the bad crowd, I suggest making your server attract other crowds. 

4. A lot of lag
You probably see this all the time in servers. A simple solution is to put less blocks. Super-huge creations cause a lot of lag and may ruin the game. And it doesn't have to be huge to be better. Small creations are just as good and cause less lag. If you want your server to have less lag, I suggest using less blocks or having less huge creations in the server.

5. Too many rules
You might fill your server with rules, to try to make the server a better place. But usually, that just makes the crowd smaller. This problem is mainly in servers where you work together to build. The server owners usually make it so you can't touch a block someone else placed, build anywhere near them, or add to their projects whatsoever. This is trying to make it so you can't damage other people's projects. But it mostly just makes it a boring server that's basically like playing in a creative singleplayer world but on a server. I would suggest getting rid of some  rules, allowing people to build together. If someone destroys someone elses project, and they are unhappy about it, maybe they shouldn't be on such a server. They should be on singleplayer, where nobody can touch their projects. Because what makes Minecraft so much fun, is that there are very few rules.

I hope these were helpful! Remember, you can think of your own solutions too! If you think this was helpful, feel free to share it with any server owners you know or use the info yourself if you own a server! If you have a server problem like the ones above you can write it in the comments and I'll see if I can help you.