Hi. I created a homebrew feat called Storm Mastery but it is not working as intended. Firstly, I used Fey Touched as a base when creating it, which seems to have lead the feat to give you the option to get the wis/int/cha ability score increase. I.E. It acts as the base feat and I am not able to change it. Secondly, I put a class requirement on it, but even though my character meets the requirement, he can't pick it.

The "touched" feats use a system we cannot access so we cannot change what it does or replicate it. You are better off trying to recreate from scratch.

Class requirements are not actually supported properly. It is best to leave it as text only and leave it up to the player to only select if they match the class.

Your player needs to ensure they have Homebrew toggled on (character builder > home page). 

Can you delete the original feat "Storm Mastery" so I can publish the 2.0 version that works as intended?

Right now I cannot publish 2.0 because it is too similar to the original one.

No, I am not a mod or site staff so I cannot. And generally public homebrew cannot be deleted. You can "create a new version" to replace the current listing with the new version, but you cannot do this if you created it separately.

You do not need to publish for your or those in your campaign to use it. Your homebrew is automatically shared with anyone in the same campaign as you and they can use it even if it has not been published and even if they lack a sub.