is perfectly understandable.
The system is broken. Believe me I think games like these should offer things for real money, to keep running, like all other popular F2P games do - but SK does it badly.
The thing is once you're a good few hours into the game, you'll be able to buy energy to keep playing to no end, negating the need to buy crystal energy. For one this is just annoying to do, buying energy with crowns to just keep playing, and secondly this doesn't benefit the company that made Spiral Knights. When you can keep going without spending real money, but just spending crowns instead, people will not feel the need to buy energy with real money anymore, at all.
Now this in of itself may not be that bad, but the following is my major point I want to make:
You are making the experience for new players bad, and people could decide to uninstall or keep playing purely upon a first impression. You are making the experience bad for new players because you're making them believe 'You have to buy CE, or you won't be able to play any more today, so buy or gtfo'. While in actuality it's more like 'Just spend the crowns you just earned for more energy and you'll be fine' once you get a bit further in the game.
Honestly I wish the company would just replace the system and offer us something different. A good example of a company that does it right is Riot games their popular F2P game called 'League of legends'. It offers you skins, champions and boosts in trade for actual RL money. People buy this a lot, me including, I loved buying me a new skin in League of legends, and yet it doesn't interfere with the gameplay at all. I think Riot games did a perfect job at designing that, it didn't [screw] over the people who didn't want to pay, and yet a lot of people did pay.
Spiral knights has enough people to try something like this, it would most definitly survive. So my message to you: figure out something different people can pay for that is interesting, I'm sure people will do it if you put some effort into it. Because giving newer players the impression they can't play unless they pay, just makes them feel like the whole 'Hey this game is F2P game' card was a load of bull.
You don't understand the energy system. In order to play after you've exhausted your mist bar you need to either buy energy with real money or buy it with crowns, and buying it with crowns means most of what earn running gates goes right back into buying energy to run more gates. You have to limit yourself to the more lucrative gates and accept a drastically slowed rate of progression.
The energy system is fine. It's the best F2P system I've seen so far.