I am going to assume that the Site runs on Java coding, If this is the case I suggest you should try upgrading to C++ It is a lot more stable and there is a lot more you can do with C++ than Java (Evidence is Runescape upgrade to the NXT Platform which uses C++)
Also if you are going to be upgrading anything on the site you should give users the ability to delete their own content from their page if they wish to. You basically say we retain the copyright to the content however we can not delete our own content though this isn't a violation of copyright law it is still quite annoying to those wishing to delete content that they no longer wish to have viewed or wishing to leave FA completely.
Another good upgrade would be to add a members list, which has several search perimeters IE; Artist type(Writer, Fursuter, graphical artist etc), Alphabetical order, Numerical order( assuming there is a numerical system) and so on. This will make finding artists easier for users.
Give users the ability to deactivate their account if they wish too, this goes in line with being able to delete content if a user chooses to deactivate their account the account should be placed in a 7 day limbo so to speak where should the user change their mind(Not likely) they can cancel the deactivation process at the end of the 7 days their account and content are automatically removed.
Mature and Adult content should be able to be viewed separately.
A grouping system for submissions by folder, currently you can categorize submissions together, however when viewing it becomes hard to select the correct submission while viewing, the idea would be that if you group the submissions together in the same folder and you click into that folder you would be able to view only the content inside that folder.
Submit as a book option, this would enable users to submit their content as 1 whole submission even though the files or submissions are separate submissions and allow users to flip the page just like as if they are holding and reading a book (Submissions of this type must be in the same folder.) As users add chapters to their submission the system would automatically recognize where the chapter belongs because while submitting the user can select where the chapter belongs with a numerical category.
Better labeling system for user submissions for categorical purposes.
You should work with the F.A.W.D Furaffinity writers directory and help make it easier to use the system to find written artists this same thing can be used to help find graphical artists as well and can be applied with my previous suggestion about adding a members directory.
Also add a way for users to be able to block specific content, with out having to just block the user, this will enable users with a better browsing experience.
The last suggestion I could pose is that you should change the way written content is uploaded to the site, Perhaps using Sta.sh like Deviant Art did, as it appears to be a solid and actually 100% of the time work method of posting written art.
These upgrades would aid in the protection of your users and yourself from attacks such as the one that happened not to long ago.
*Add security questions, set preset questions for users to pick from or allow the user to set their own custom questions
*Add G-Auth or Authy Security system into the sign-in and allow users to select to be able to stay signed in for 30 days if they wish too and remove the captcha system from the sign-in process also add G-Auth or Authy Security to the registration process
These are just suggestions of course and most likely will be disregarded however I hope that they are taken seriously. Some of these suggestions may have been mentioned before.