How was balancing done in ff11? Poorly. Throughout pretty much every stage of FFXI's life, there were top tier jobs that were preferred for certain kinds of content. If you didn't have one of those jobs leveled, it could be very difficult for you to do that content. You pretty much had to be part of a linkshell that tolerated your unfortunate choice of job. Worse, since nerfs and fixes occurred from time to time that shuffled around the job tiers, even if you did level a top tier job it could lose its place later on and become a low tier job.
As for specialized equipment, FFXI had the Relics. For a long space of time the Relic weapons were hands down the best weapons of their type anyone could get (well, with a few exceptions; the WHM and BLM weapons weren't too useful since they didn't really do much to boost magic). It wasn't much of an exaggeration to say that a player with a Relic weapon were worth two without. So why didn't everyone insist on bringing Relic-owners to do content? Simply because Relic weapons were HORRENDOUSLY difficult to obtain. It simply wasn't feasible to insist that party members all have Relic weapons, because there were only a handful of Relic owners on each server.
Later on, Relics became much easier to obtain, and at that point, all thoughts of balance simply went out the window - particularly in the case of Paladin and Bard. The Paladin and Bard Relics boosted those jobs so ridiculously that any PLD or BRD player who DIDN'T grind out one of these babies might as well not play the job at all. No casual player could play PLD or BRD; the relic grind was easier now, but it was still WAY outside the realm of casual play.
To a lesser degree, the balance issues in FFXI were part of the reason that the crafting system in this game has been so thoroughly castrated. In FFXI, there was plenty of equipment crafted with rare, expensive ingredients that were so useful for the jobs that could use it that players would be turned away if they didn't have them. Things like the Scorpion Harness - DPS gear far superior to anything else that could be worn at it's level. Noble's Tunic, one of the few sources of MP regeneration available to WHMs, and with a 10% Cure Potency stat to boot. The elemental staves, one for each element, each with a huge potency and accuracy bonus for their specific element. Because of items like these, the crafting system in FFXIV will likely never see any utility beyond fluff and glamour, unless SE overlooks how useful the equipment can be (such as the ilvl 110 accessories).