On to the problem you're having, I use Pixelmon as well with a TON of plugins and with just my 3gb server everyone seems to be lag free for the most part except when we World Edit a large amount of blocks.
May I ask which .jar you're using with Minecrafted? We had some problems figuring out which one worked correctly with Forge since they don't specify. (Craftbukkit ended up being the working one)