I miss the immersion that you get from real diving (no pun intended).

• add more layers of waves crashing on the shore.
• add a trail in the water surface when moving through water at surface level.
• add a scuba mask hud in 1st person view when diving.
• add water dripping graphics on said scuba mask hud when the player emerges from diving.
• add a wealth of clutter/particles/bubbles under water.
• add more bubbles and a trail of bubbles after the player that floats towards the surface when he swims under water: http://www.youtube.com/watch?v=pk2e6E8HwxY (never mind the music).
• the diving bubble sounds when swimming under water is good, but needs to be louder, more intense, and not fall completely silent at any time under water.
• tweak the color filter underwater even more, maybe even blur the vision slightly when under water.
• when enemies fire upon a diving player from the shore, their bullets should penetrate the surface, slow down and trail underwater. Damage should be very low, almost ignored if they actually hit you under water. Here is an AK47 fired under water (go to 1:59) http://www.youtube.com/watch?v=cp5gdUHFGIQ - here is a Glock .22 http://www.youtube.com/watch?v=502KryEguA0. These are also inspiration for graphics of player guns firing under water.

All these, and probably more good suggestions in the comments, should be implemented to achieve a better immersion experience in underwater missions.