Okay so where to start, first and foremost I think the biggest issue with the game atm is the fact server populations are so unbalanced, while on the surface the numbers may look healthy, most the servers have extremely high jp populations and despite your wonderful auto-translate system, many players don't feel comfortable playing interacially (yes, I'm fed up of being told jp-orny), this leaves most the EU/US (read especially EU) with little-nothing or no one to play with as things currently stand, I'm not sure what to suggest as an immediate fix to this issue, perhaps offer regional-only servers for people to transfer to which (hopefully?) have a higher target player base?
Secondly, instancing is -terrible- there's just no other way to say it, every piece of content that requires you to entered an instanced battlefield is congested to the point I'm typing this while sat in front of the AR2 entrance spamming enter attempting to get in. Yes, its great when you pay for a service, you can't actually use. Absolutely great.
Well thats about it and lets be clear, I still enjoy FFXI (into my 9th continuous years and still enjoying it, I must be a glutton for punishment), the game concept I enjoy, the current serious hardware and software issues leading to 30-60min wait times on entry (or complete inability all together) to actually play the content paid for I do not.