I'm just going to say bits of pieces of everything I think is good. I will start by breaking down the OP.
First off, read this post
http://squidboards.com/threads/how-defense-up-damage-up-seem-to-work.1258/#post-29389
Secondly, DMG/DEF up are situational at best. To elaborate on this, DEF UP is very good for say, the JR/Aerospray guns. This is because, their must common enemy is the .gal series. With one DEF UP, you die in 3 shots, instead of 2. Giving the JR/Aerospray a real fighting chance. Ofc they lose at a distance, but with mobility and ninja swimmer, closing any gap is easy. I don't know any situational occurs for DMG up atm.
Run SPD UP is good, since the boost is fairly large. Do know this increases your run speed by 50%. Swim spd up is great, however, the boost is half as large as run spd up.
Ink savors are more than likely top tier. This in combination with a ink recovery er two as sub-abilities, is amazing.
Ninja Swimmer and Cold Blooded are going be top tier. I can see Cold Blooded being higher than ninja as the meta evolves tho. For those of you, who are ill-informed on Cold Blooded... It reduces the amount of time tracking items apply to you:
Point Sensor 10sec->2.5sec
Echolocator 12sec->3sec
Ink Resistance is one of the best skills in the game. When you are normally in enemy ink, your run spd/jump height is lowered to 12%. You also take a large chunk of DPS while standing in it. With this ability however, your run spd/jump height are lowered to 80% broken
Haunt is really good, if you are always in the heat of the battle.
I'll probably come back and revisit this thread, as more posts are dropped.