I’m going to offer up my opinion on what the Everfree Forest is and what the ponies are doing about it.
IMO, the Everfree exists because the fight to imprison Nightmare Moon had devastating side-effects. The battle was at the Palace of the Royal Pony Sisters, and the surrounding area was somehow made unsafe for ponies. Evacuated and abandoned (with Celestia transferring to Canterlot), it was left unattended. Between nature and magic, it overgrew and spawned all those creatures and problems. Over the centuries, Celestia sponsored what ponies she could to try and reclaim bits of the Everfree, such as Sweet Apple Acres and Ponyville.
This means the Everfree is a small example of what Equestria would be like if the ponies weren’t managing it. There should also be the remnants of buildings, roads, and other unmovable or forgotten things scattered about, assuming they could survive 1,000 years. And with Luna restored, the Royal Sisters have the capacity to make more than an opportunistic effort to reclaim the area.
Thoughts? Counter-arguments?