But isn't that organization mostly used for political persecution, only under the guise of human rights' interests? Haven't they only gone after politically-unpopular-in-the-west entities, and never after the real egregious human rights violators?
No.
You may have a misunderstanding of what the ECHR is. A party can make an application to the ECHR against a member state of the Council of Europe (not the same as the EU) that that member has breached an article of the agreed European Convention on Human Rights. They don't "go after" individuals.
I see, thank you. I now see with which organization I had confused the ECHR.