Some of the abilities listed by the OP are very useful (seriously, why are they on that list?) but you do have a point on some of them being utterly worthless. I'll chime in with my two cents.

Freeze / Blizzard II
Oh god did I ever lament the day when SE in their undoubtedly infinite wisdom decided to nerf our Blizzard II spell and instead buff Freeze to be only slightly less worthless than it already was. I couldn't honestly care any less that they made it cross-class. It was reduced to a useless waste of space then, and it's a useless waste of space now. Pitiful damage and a bind effect which, in case anyone wasn't paying attention in class, is worthless in 90% of every battle ever.

Bind *was* useful back in the day because being hit for small damage didn't unbind every target. Now it only takes a tiny scratch to break binds, making it the most pointless status in the game. Giving a useless skill to more classes doesn't magically make it any more worthwhile. It's still a junk skill, it's just spreading the misery around.

Freeze is basically the same as the original Blizzard II, only it costs more, takes longer to cast and is basically useless in almost every situation bar perhaps 2 unique circumstances. It has graced my hotbar for all of about a day, and now shares relegation alongside the nerfed Blizzard II.

Presence of Mind
Seriously, do I even need to say why this is a stupid skill? Let's start at the top: It has a cast time. It has a short duration. The speed boost is barely noticeable. The total time saved by using the skill is scarcely more than the time spent using the stupid skill to begin with. Lastly, it's entirely pointless to even use this skill unless whatever spell follows is practically SPAMMED for the whole 10 seconds its active. That's literally the only way to make it pay off.

If you need to rely on this skill to spam heals, you've already lost.

Apocatastasis
No self-cast. Stupid restrictions on reuse. Utterly negligible damage reduction. It's like putting a bandaid on a severed limb.

Cure III
Rarely used for the obvious reason that its incredibly tiny radius means it won't hit anyone but the target you aim it at on 90% of all fights. Barely worth casting at any other time, even with Overcure. Seriously, give us back the old Overcure. At least when it hit for criticals it meant something to use it instead of Cure II!

Ifrit-Egi
Once you get Garuda, Ifrit is pretty much a window-dressing. It's a sad fact that Ifrit simply doesn't have the skills to outclass Garuda in sheer DPS, and lacks the tank ability of Titan. This makes him easily the least used Egi of all, at least after the 15 levels it takes to upgrade. His signature move should be devastatingly more powerful than Garuda or Titan's, being the DPS of the bunch. I think I could even live with it being a single target ability if the damage meant it was worth using on a boss at least.

...those are just a few from the classes I've levelled. I can't say I've found a single useless skill on Paladin yet. Pretty much all of them are a staple to keep myself alive and, by extension the party.