i'll start off with the CE suggestion, make a rare drop, rarer than tokens... That gives you a mist tank. They can only be found at the terminals/difficult missions, giving the player more time/levels to do!(I know 3rings that it goes against the freemium idea, but it makes it easier on us, the players.) OR you could find about 10 like you find moonstone and such, bring it to the end of the level and you can get 10 CE on the next level! I mean, Crystal energy isn't exactly Crystal energy atm huh?

SUGG #2
I know the core battle has been suggested multiple times, and I think a few years ago someone suggested that the bosses come back for revenge, stronger than before. That you've taken into consideration and made shadow levels. But... Shadow levels arent enough. My idea for the battle is:
1. Have 5* armor and such.
2. Have 1 shadow key.
3. there is a terminal covered in TV's displaying locks, use the shadow key on the terminal. The terminal reacts to the key and sends a signal to the core, surging you down to the depth 50. You fight your way up to depth 45, you fight snarbolax, but even stronger. at depth 44 theres a terminal, immediatly afterwards the ice queen. After that is another terminal, and Dark Vanaduke. Finally the core, which cant be damaged until it comes out of it's... core. You continue to hit the heart until it's defeated, summonning more shadow things. It gives one Core Token.