Raw GDP is an absurd proxy for standard of living, you're comparing a country of 70 million to a country of 1.5 million. At the very least you'd need it to be per capita. Maybe PPP adjusted.
Thanks for pointing this out and you're absolutely right. The per capita comparison is much better, and shows Estonia's economy at 54% smaller [1] (Bulgaria makes for an even starker contrast at 82% smaller per capita [3])
Edit - As a final edit, the largest disparity across standard of living in the EU is between Luxembourg and Bulgaria, and comparing their per-capita GDP shows that Bulgaria's economy is 93.2% smaller [4]
This is still a considerable difference between the two countries and yet not everyone has fled from Estonia/Bulgaria.
The point though is that there is a very big spread in the standard of living [2] across the EU and yet mass migration is not occurring.