Not Quite There
Here's the thing...you have this excellent environment, with unique looking creatures and a very detailed backdrop, and you have the ability to explore both the sea and air, a twist I was pleasantly surprised to discover. On top of that, there is plenty of things to collect; purple pills for points, yellow pills for "God mode", white balls for boosts, and I already covered the wings. So why does this game get boring so fast?
The problem is we never get to engage the environment or the game. Once you've snagged the yellow pill and the wings once, you've pretty much done the most exciting things in the game; there's no incentive to continue other than to gain more points, but lets face it, who really cares about points? I never look at the scoreboards myself, escpecially considering 99% of the time somebody hacks them. What's more, your little guy never gets stronger and only has one life, so instead of exploring/enjoying/etc. the lush environment, you're focused purely on evasion.
My suggestions? There's the obvious "make the fish grow larger so it can eat larger fish" route, which admittedly would work, but that's been done before. What I do love is this whole "grab some wings and explore the sky" concept, so here's my grandoise vision for Blue 2-3...
This time, there are four different spheres you can traverse, all of which are stacked vertically: earth, ocean, sky, space. You enter each area the same way you do in this game, by picking a power-up, except this time, the power-up lasts as long as you stay in that area. In the water, obviously, you swim; underground, you have a drill and you dig; in the air, you have wings again; and in space THRUSTERS mwah ha ha. You have seven stats, which you can increase as you level up (by eating other fish); size, speed, acceleration, wings, thrusters, drill, and tailfin. Upgrading size, obviously, makes you larger and you can eat larger fish. Speed and acceleration should be obviously. Upgrading the last for stats will affect how well your creature maneuvers in the four spheres. Here's the catch, though; getting eight purple pills still multiples your score, but the pills will be split evenly amongst the four areas. You could make each sphere of movement either have different controls or different types of enemies; either way, you could upgrade your drill if you suck at underground movement and leave your wings alone if you're good at the air.
Damn, dude, as Jimmy Neutron would say, "brain blast." Yeah, I just quoted Jimmy Neutron. Deal with it. Seriously, this long response is brought to you by boredom and insomnia. Good luck, kiddo.