There's a lot of useless skills that could be amazing skills with just a small tweak. surecast for example is absolutely useless. but if it was tweaked to allow you to cast the next spell uninterrupted while moving. it'd suddenly be an amazing spell and a great help for many blackmages, surecasting blizzard 4 for example to keep there enochain up even if they have to dodge mechanics.
All crowd control is useless by game design. shadowbind heavy freeze, sleep repose. a blm will never sleep anything instead they'll just fire 2 the whole lot till its dead, nothing hits hard enough to warrant sleeps or any form of crowd control and everything is simply rounded up and aoed down.
then you have skills that are used but totally innefective or not used for there intended purpose. pacifys, stuns, silences etc, the only thing these are ever used for 99% of the time is a small dps increase, so when you find mechanics you could stun you inevitably can't because the boss is immune because everyones been spamming stuns for the small dps boost.
silence is the same. think I can name 2 things of hand that silence has ever been usefull for. high voltage in very early coil days and requelling mist in the forgall fight in weeping city. again blunt arrow is only ever used as a dps increase 99% of the time.
then you have situations like paladins. where a good portion of its toolkit is basically useless in a remotely decent group. cover is one example, divine veil also. it's a pretty strong shield admittedly but it isn't really needed or usefull that often. if you pass a dps check before big aoe damage that damage is trivial. and divine veil is a joke, if you fail the dps check you wipe regardless of how many shields you can throw up.
so many skills are made useless simply from the way content is designed