If you want to report an issue, PLEASE report a single issue at a time, so that they may be kept track of individually.
Comments on the errors in the order they appear in the post.
SimpleChannelHandlerWrapper exception: Not much useful info, if any at all. Looks like a networking issue.
Exception in server tick loop: Doesn't look like pixelmon related. Make sure that forge and mods/sidemods/plugins are updated properly.
FMLIndexedMessageCodec exception caught: Again, seems to be a networking issue, although the last one might help.
Unable to read a class file correctly: Whatever launcher.jar is, it's most likely corrupted. Replace or reinstall.
Broken pipe: Yet another networking error. This one is pretty generic and there's virtually no useful info. Some people have had luck by modifying the vanilla jar that comes with a forge installation.
Destiny Bond: Known issue, fixed for the next release.
X moved too quickly!: Disable movement checks in Sponge's configuration.