Atlantean Vel'Koz
Model
Well, since Vel'Koz resembles an octopus (and a bit of clamp), and the body is sort of encased within an armor - he could have suction cups in his tentacles, and the body covered with the Atlantean style armor. The Eye, could have this yellowish/light orange tune with some crazy contrasting pupil, the sort an octopus or perhaps a reptile could have. The lesser eyes could be potentially different, such as pearls, jewels or what have you. He can take them out at will, so inorganic materials aren't out of the question, I'd think. The ideas for body's color and patterns are kind of endless, depends what kind of color scheme would be fitting. There could be additional lesser tentacles on his body. The prime tentacle's could have some bronze'esque ornaments on their tips (harpoons, tridents, claws, plain caps... you name it).
Abilities' Visual Effects
Basic Attacks - Well, I'd like to say water effects, but ink attacks sound pretty awesome. The problem might arise with these short (fast), projectileless attacks.
Organic Deconstruction (Passive) - Instead of a triangular symbol, it could have some round crest, consisting of 3 pieces (duh). Like an ornamental bronze plate or something more complicated/angular. There are lots of possibilities.
Plasma Fission (Q) - How about an Ink blob leaving the victims covered with the black oily goo for the slow's duration?
Void Rift (W) - This one might be a bit tricky. With plain water effects, it sounds pretty boring. Perhaps a deep sea crevasse with seaweed floating on the side etc. The second damage instance could be a... volcanic eruption? I'm not talking about a big lava burst, but a brief flash followed by smoke/underwater dust or what it would be.
Tectonic Disruption (E) - Similar to Nautilus' Riptide or Depth Charge explosion, I'd imagine. Don't think this skill needs much touching outside of its color.
Lifeform Disintegration Ray (R) - Imagine him firing a powerful jet of water that cuts through everything. Or it could also be ink blast, like was suggested bellow.
Sound Effects
Well, the visual effects need obviously sound effects to back em up. A new voice over isn't needed, and as for a voice filter, I think it's not necessary.
Overall I think Atlantean theme would fit Vel'Koz perfectly. That is just me however, so please, share your thoughts. It doesn't necessarily have to be Atlantean. A Deep Terror or some other sea theme is practically the same.