Like every other person from Edolas, Mystogan does not have innate magic. If he did, he would have been expelled from Edolas like the Exceed were. Instead, he gets his magic power from magic items, primarily the large number of staves he carries on his back. It is possible that he obtains these items from Earthland magic shops, however three things point to this not being the case:
- The magic shop we see in the first episode only carries novelties, such as something to change the color of clothing. There are powerful lacrimas later in the series, so we can't draw a definite conclusion on whether the shops would have the powerful sort of things Mystogan uses.
- Edolas's magic items are more advanced than Earthland's. When Natsu's group went to Edolas, they marveled at some of the things they saw and mentioned this. Edolas even has a mechanized dragon.
- Mystogan's magic pills. These unusual pills allow Earthlanders to use their magic in Edolas. There wouldn't seem to be a reason for these to even exist in Earthland, so it would be strange if shops were selling them.
These three reasons lend support to the idea that Mystogan at least partially creates his magic items himself using his Edolas knowledge. And if this is the case, it might explain why his magic power is so great even though he has no innate magic.
On the other hand, Jellal was able to imitate Mystogan's magic at the Grand Magic Games, so maybe one can obtain those magic items in Earth Land. Though if so, it begs the question why there aren't more S-class wizards. Jellal's imitation could possibly be explained by Earthland's magic advancing in the seven years, or by Jellal somehow obtaining the staves used by Mystogan.