Every time I try to use /l to log in, it tells me that I don't have permissions, this is because essentials uses the /l command to display the list of online players. How can I fix this problem?

Conflict with anothers plugins too. Maybe we can disable this aliases?

/l is not Essentials command. If you are using MyCommands, then delete list alias from examples.yml.

This / l conflict with localchat. / l are use all the time to talk local, so write /l is more fast than /localchat all the time, instead / login are used just one time when login only. I'v done my compile removing that, but have a config for that will be great

I think you can resolve alias conflicts with Spigot's commands.yml, https://bukkit.gamepedia.com/Commands.yml

IMHO on our side it's not easy to make it configurable because the plugin system requires us to define aliases in the plugin.yml that we ship with the JAR, so we don't have a way of dynamically adding or removing entries in there apart from offering multiple JAR files (which doesn't make sense for such a distinction).