Shogun may have been made with a small team - but it was also done on full-time. EB's people mostly work in spurts of activity, when we have a lot of time on our hands. There are many intermittent breaks when other stuff is happening, like work, getting married, going on an archeology dig etc.

If you want a "game made entirely by modding", perhaps you should try one of the many Rogue-like games. I'm fond of ZAngband, myself.