Honestly, what's good does depend a lot on what your weapon choice is, so it may very well be easier to list what isn't so great, for any load out.
On this, the abilities I currently have no use for (my go-to weapons being the splash-o-matic and ttk):
Quick super jump / stealth jump - I tend not to super jump, so would be wasted on me.
Defence-up - since this is countered by damage up, I tend to assume that anyone using the weapons that are hampered by a defence-up will have the good sense to equip damage-up, and so it will be wasted slot (though this is often not the case).
Ink saver sub - the subs that I use are so ink-hungry that the effect of this is pretty negligible - all I'd get is a few extra shots after throwing the sub before needing to replenish the ink tank, and I don't seem to miss those.
Last ditch effort - the abilities that this boosts aren't so useful for me, since my weapons are already pretty ink efficient.
Haunt - it's a fun idea, but as it stands it seems a little gimmicky. Also countered by cold blooded, so won't always be effective.
Bomb sniffer - I've not tested this, but since bombs/mines are already pretty well telegraphed anyway, I don't feel like I'm missing out.