While there are probably long lists of things folks might individually list as missing in any game, there are two things I often find pronouncedly missing in EQ2:
1. The absence of any kind of scripting API. You don’t have to struggle with SWIG or tolua++ to Git’Er’Done. Just expose what you want exposed with your own glue functions. That way, there’s no risk of anyone doing what they’re not supposed to. Lua, Javascript or Python make good engines. Python might be a bit much.
2. Lack of a way to link tradeskill lists. EQ2s crafting is good, the tradeskill business is thriving, its downfall is when someone asks “can you make …”. Dude. I have a HUGE ass list of things I can make.
kfsone's pittance 
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I usually find that when some random dweeb comes up to me and asks “can you make x?” it’s more a case of a 10 year old brain unable to distingush between “do you have the ability to make x?” and “will you make x for me?” with one being interchanged for the other.