Nobody gave a good reason for the fee yet.
There has to be a fee because there was always a fee. I hope you are not that inflexible in reallife.
Give good reasons and I'll shut up
It encourages you to think through your plan before actually putting it to use.
I understand no one can make the perfect deck with their first try, but you have to be intelligent enough to actually have an idea first before you just try things.
Also, to get away from deck experimentation itself, when you already have a few decks that have different purposes (e.g. coin farming, pvp, false gods, card farming) then most likely you need to switch between marks to use the different decks. The price makes it so you can't switch between each thing without even a little of a repercussion.
You guys are way to whiney about this "waaaah there is a 100 coin fee to switch decks." You're forgetting that every other aspect of this game is directed toward working for your goals; the 1,500 fee for upgrades, the low coin income... the metamorphoses cost just makes your goals that much harder to achieve, which makes them that much better in the end.