First of all, neither will improve performance with Skyrim. Skyrim's performance issues stem from poor design decisions and a lack of optimsation resulting in the game needing more memory than is available on the PS3, Bethesda's answer to this little problem was a massive swap file in the mandatory install. While a faster drive will give a faster swap speed, it won't give you a noticable difference in performance, the game will still break down when it reaches that memory threshold and get progressively worse after that.
Second, if this hard drive is going into your PS3, as in internally, then you don't need to worry about file format. The PS3 uses a special Sony patented file format and encryption and the console will format any newly inserted drive to that format during the setup. It literally is a case of insert drive, switch on console and then wait for it to finish.
A 500gb drive is definitely worth it if you have a lot of games, after formatting and encryption you're left with about 415gb, so if you buy a lot of stuff from the PS Store or have PS+ it'll prove itself a worthy investment almost immediately. Anyone with PS+ will find a bigger drive pretty much essential, it's also great to not have to delete an old game every time you buy a new one which used to be a huge problem for me with my 60gb fat and even my 120gb slim, but just for Skyrim? Nah.