Anyone have anything they'd like to see in the game if it was possible?

The thing I find myself missing most is a photoalbum with all the aquaroids the worm has taken of the fishies. It would be nice if there was a database / album / scrapbook were the kitty and worm team of the Cat Nav collected the photos of fishies as you encounter them.

I would like to see a shop where you can upgrade your submarine between the levels and buy new power-ups (e.g. a shield would be nice).

Yeah, I agree. Some kind of upgrade system. Though a lot of Flash games take the route of turning what should be an arcade-style game into a grind quest. A simple solution could be to have a cash pool, where only your high scores are counted once each.

No idea on the particulars, but something like that, yeah.

EDIT: Maybe an alternate energy meter attack option, like a bomb or temporary shield. I also found myself wanting to have a speed boost button (with some kind of resource)

I'm also finding that the game doesn't have much of an incentive for saving more than one milk mine, unless I'm not seeing something. Score and bragging rights is one thing, but I feel like a stronger incentive should be used.

Ex 1: A store to spend money equal to the sum of your high scores, with things like power-up duration, starting health, etc.
Ex. 2: This next one seems more "arcade style" to me - a life system where both your submarine kitty and the milk mines both count as "lives". This would probably require a rebalance. A perfect run would be the same in both cases, but a low-scoring run where you only save one mine per level would just be a failed run in this new game mode.

Maybe change the interactions around a bit more.

* Invulnerable kitty tanks destroy enemies on collision? Deflect energy shots?
* Bullets can destroy missiles?
* Pufferfish explosion can hurt you too?