Just some "simple" ideas to be hopefully added to the game
Firstly, who here has activated a mechaknight? I personally have never because it puts my CE at a strange number for buying stuff. So what about being able to buy an energy wrench for CE? This wrench should be able to repair broken mechanisms for free after a set time such as broken mechaknights or some generators that power bridges to loot. The mechaknights just kinda sit there and do nothing but perhaps this item would encourage players to use them more, or perhaps explore the clockworks more (its lonely out here ;-;). Of course its a steep up-front cost but over time perhaps it would be cost effective.
Next is residual heat. Everyone gets annoyed that they levelled up a weapon to juuust enough heat that any floor would be enough to level it up, meaning that any leftover heat is wasted. How about any leftover heat is transferred to the next level? However if something is overheated it cannot gain more residual heat and will cool over over time, loosing heat and still being unable to get more. This means that you have to forge the weapon as soon as possible to make the most of this residual heat.
Also, how about quests that take place on some floor in the clockworks instead of prestige missions. Currently prestige missions throw you into the fray rather quickly after a few floors and give minimal rewards. How about giving players a challenge by giving them access to danger rooms for free. Or rescuing some knights somewhere somehow. Accepting a mission would tell you the gate and the floor the quest is on and going to that floor would guarantee the quest objective is there. Of course the missions would be ranked for their difficulty.
Anyway, just some thoughts.
You know, now that you mention it, if we could have what amounts to a mini mist energy tank (max size 15) that fills up from residual heat, with the max size of the tank increasing depending on what prestige badge you have, that would solve pretty much every problem you listed while incorporating them all in the same system.
In the olden days you had to wait to get energy. With this change, you have to "heat" to get tiny amounts of energy. You'd use said energy for tiny discounts on the supply depot along with powering up mecha knights, discounting spark of life activations, bribing king krogmo, and opening energy gates.
Letting prestige bump your max heat energy tank to, say, 25, would be a wonderful additional as well. Suddenly, you can bribe king krogmo for free every once and a while! It gets more players willing to spend on a few small things while not giving them tremendous discounts on any item.
Having this heat energy slowly dissipate over time is another interesting way to do it. I would say you'd lose 1 heat energy every hour, however if you gain max heat energy and then "double" that amount (remainder does go to technical waste), it wouldn't lose the heat energy for 24 hours. Each time you double the heat energy at max, it resets the timer (rather than increasing it by another 24 hours).
This means if you play FSC like, 3 times with gear that you can't level up, you have a bonus 25 energy for the day. In a way, it acts like a "login bonus" that you obtain for playing the game - something that the prestige system tried to pull off but doesn't provide any incentive to actually do.
Sorry for kind of taking your suggestion a different direction, but it inspired me to write this. :)