What are the purpose of Energy Wells

Since you can purchase crystal energy with the in-game currency, it seems like kind of a moot point. There are times where you will need more than 100 energy, for crafting or such. Now you could choose to just not do this, and then you wouldn't need crystal energy. But you can also choose to go farm some crowns, then buy the crystal energy that you need.

So you can certainly get through the game without ever spending real money, and if you aren't spending real money, you should just look at crystal energy as another in-game resource which you occasionally need to replenish with crowns.

The Spiral Knights Wiki has the skinny on crafting:

Alchemy Machines are located in Haven, Moorcroft Manor, and Emberlight. Haven has several Alchemy Machines which can be found in Guildhalls, the Bazaar, Arcade, and the Town Square. The cost of crafting an item depends on its star level, and generally doubles with each additional star.

• Alchemy Cost:
• ★☆☆☆☆: 200 crowns/ 10 energy
• ★★☆☆☆: 400 crowns/ 50 energy
• ★★★☆☆: 1,000 crowns/ 200 energy
• ★★★★☆: 2,500 crowns/ 400 energy
• ★★★★★: 5,000 crowns/ 800 energy

Usually, crafting is much cheaper than buying the item pre-made from a vendor, and also gives the added possibility of creating a unique variant (see below). Pre-made items increase in price as their star level increases. Thus, items with a high star level are generally cheaper to craft than to buy pre-made.