I was thinking a bit and I have a bunch of random suggestions.
1: Rebalance Angel Isles missions.
It's clear that the Angel Isles were designed for a different game. In Tier 1 they're OK, since that's what they were meant to be like (they were from the Skies Under Cradle mission), but if you get them in the Arcade in Tier 2 or 3, they're complete chaos.
Don't get me wrong: I like the levels, the music's amazing, but some sections are just impossible.
2: Mini Mist Tanks.
This is just a little way to encourage small energy spending: you have, say, 10 energy per day, and the only thing you can use it on are energy gates and mecha knights/auto turrets. Right now it's very unlikely you'll make a profit by opening a gate, and I think this would be a good retro-fix.
3: I don't have any other suggestions...
Angel Isles? Do you mean the Aurora Isles?
Aurora Isles aren't too bad where they stand. They were from an earlier part of the game's development, however I think they scale pretty well. They just have a lot more walking to them than other levels, so I'd really enjoy more monster spawns or gates when backtracking to make it more interesting/faster.
Mist tanks would be pretty neat. The number should be small and still take the same amount of time as before to recharge (ie, 22 hours for a full tank). There's lots of stuff that we don't use energy on because it's a premium resource, so having a tiny amount of it for free allows us to open gates all we like without feeling bad about opening them.
I think you should get no more than 15 energy, and no less than 10 in these tanks.