I thing such settings would be intresting knowing that the author must try and use other races and not ponies. Now what kind of effect would it have?

Magic and a vast verity of spells could be casted and done by the unicorns. If they are gone, only a few creatures will have magical capabilities. In another word it will be rare.

Climate changes are unpridictable. Considering that pegasus are gone, they simply lost the ability to change weather.

Lack of food!

Earth ponies had a big part in faring industry and not just for themselves but also for other races.