Missions should give you Crystal Energy when you complete them so that you can alchemize your weapons the weapons we get to actually be able to use the recipes we get. ( if this comes in a update we should get the crystal energy that we should have gotten from completing missions.
If Crystal Energy was given out in missions, this would do a lot of damage to the in-game economy. OOO (Three Rings) needs people to purchase CE with real money in order to stay in business. I understand that it sort of makes sense for them to give new players energy to guide them further into the game, but the fact is that energy needs to be purchased. You can buy energy by trading crowns for it after clicking on your energy total in the bottom right corner.
Also, if CE was given out in missions, people would be able to keep creating new accounts to get more energy from them. Since CE can be freely traded, this would essentially break the game.