It will be faster to just create a new game, that has the things you want. It's an 20+ years old game by now, and it shows everywhere you look. You would need to overhaul pretty much everything at this point.
Visuals and overall features are outdated, even by early 2000–2010 standards. Classes are badly designed and balanced, abilities, equipment, and Quests are for the most part underwhelming, flawed or not existent.
PvM is plain, lacks anything that could make it actually fun, especially compared to other titles of similar times - Dragonica, Maple Story or even WoW.
While PvP had some game modes with potential, the core flaws of the game did really bottleneck them. The Introduction of CS items that are out of place or plain overpowered, Awakes or rather having an abundance of stats and values everywhere you look, turned every most aspect obsolete or unbalanced. Remember the actual title of the game? FLY for fun, where you rarely even fly, or have interesting things while doing so - just another obsolete aspect of the game. It lacks a clear direction and exploration of it, many unfinished features.
Even to this day you can find remains in the code of unfinished stuff, not to mention - countless game breaking bugs, exploits and major issues, which even got worse with each update and new addition. Just think back on the state of duping, and exploit abuse over the years.
For most people, v6/v7 was by far the best time to be in this game, i highly agree to this. Having to actually use your skills to level them, to the PK system itself. Aspects such as the Quiz, Rock-Paper-Scizor, Rainbowrace or Guild street brawl are forgotten nowadays.
While you could try to patch those issues, the core remains flawed. Why would anyone play this game, if they aren't touched by some nostalgia?
It went through many publishers, awful patches and cash grabs, that it is basically dead for quite a while - probably since v14/15 and the merges of the servers.
The Pserver took quite a turn too, in the early days, not that many did have the files, skill or hardware to open a server, which made it to an arms race for each server that had those. Now, everyone has had a server, and they vanish as fast, as they appear after a short while - why would you stick around after investing time and money as a player into them, just so they vanish without a sign.
For things i'd like in flyff? Removal of all the garbage that was added past v6/7, finish and add onto the systems and for the love of Boboku, fix the damn bugs. Rebalance each and every class, their skills and equipment. Make them unique, less is more, as long as it's properly made, even 4 classes can be fun - you could even remove the typical class direction. Have it similar to Skyrim, and be able to master different areas. Meaningful Quests, other then kill and fetch ones.
Once you have a solid foundation, you can do quite a thing to it. However, nobody will go this route, ever. Just have a look at the promising universe flyff project, that turned even worse than the old official one.
Wall of text ends here, just basically just overhaul everything, or simply create it from scratch. There is no saving in flyff, only a handful of passionate people remain, even fewer that still have the knowledge or are willing to do anything with the leftovers.