They mean server issues when they say server issues because from the get go the servers have been a problem for ARR in some capacity (either Level3.net fucking up or the timing being fucking 1-3 seconds instead of 0.1) and I'm pretty sure if it was simply "PS3 issues", FFXI would suffer from the same if not worse problems being a PS2 game, despite the whole "oh you can't compare the two!" if you see how much data XI's gear require, it would
choke on it's own design to the point the game wouldn't even work. Pretty much all of the lead designers (Graphics, programming, sound etc and including Yoshi) have been clear about PS3 issues and server issues and never muddled the two. Much like back in the day "PS2 Limitations" was SE's way of saying "no" because all of a sudden they can get around those "PS2 Limitations" while still technically supporting it.
Take for example:
Gear like this in XI shouldn't exist if it's a simple "console limitation" given its age and the fact XI's datastreams are capped to 56k, because that's quite a bit of data being sent back and forth, and that's just one piece. Throw in gearswapping, the fact it's a game developed in 1997-2001 and well...when you rush a game..it's no surprise they're now taking the time to optimize it further. The only thing that they're not being honest about is: "We're looking into allowing you to use retainers for blah blah" instead of coming out and saying: "We're forcing you to buy retainers because we want more money."