And do you understand that it's literally impossible without a VERY huge amount of work?
All characters needed to be rebuilt in 3d Sprites, All vanity they released in last 9 years all need to be redone in 3d format, that Ugly UFO hat will look even uglier in 3d
?
The region needs to be coded(well if they add 3d means we need gen 6), optimised for low end devices, as we all know PokeMMO runs in low end devices so if they add 3d graphics the game may crash or won't work in low end devices. So I don't think adding 3d is better in any sense it will just take a lot time for Fancy looks but won't do a thing in real game Content except PvP side since we get gen 6 mons.
As they planned for dungeons and johto since 1998 so I think adding them is way better than 3d graphics atm.