Ragnarok Online is a fantastic game and if you're adding a custom that makes some large portion of it obsolete, you're bound to run into issues.
My own struggle has been trying to do the exact opposite; bringing the game back. Renewal turned obsolete most of the content, skills, mechanics and items in favor of something narrow and mindless, so it's been a a constant struggle.
I myself wouldn't play on a renewal server that hasn't at least tackled the basic issues. Pre-renewal is a different beast though, but there are still a few rough edges which many complain about, yet apparently nobody has been bold enough to polish.
At the end of the day though, there isn't a single server out there which doesn't have a bunch of custom features, and the definition of what's custom is rather hazy. kRO, jRO, iRO and all the license holders have something of their own going on, so there isn't a clear definition of what's "official".
It is also rather common for players to think than some decade old emulator bugs are the proper behavior, or that fixes of official bugs (which might have been fixed on Aegis years ago) are horrible custom changes. It usually boils down to what benefits them and what doesn't.
Private server owners have the benefit of being able to improve the game in many ways, so I find it foolish to waste that ability. More so when you consider that the game is now a dying cash cow which Gravity still attempts to milk.
In my eyes, the direction they took for the game isn't something worth pursuing.
I do believe that custom changes shouldn't stand out too much, they must feel right, fitting the game's general setting and "feeling". Successful changes are those which players assume to be the norm.
This is harder to do with custom content though, unless you recycle resources in a clever way or have a really talented artist in your team.