I've considered it as a Spanish resident, but don't you have to live six months there to be considered a fiscal resident? Are people regularly operating them from outside Estonia?
Basically it would be best if you have no customers from Spain or country of your residence.
As others have said, it mostly makes sense for people outside of the EU. If you have personal residency in Spain then it is questionable whether the easier paperwork in Estonia will offset the need to do some paperwork in Spain as well.