Isn't that the definition of a good compromise?
I mean, each EU country is fighting to get itself the best deal, to bolster its position over other EU states. There is no way to make it so that everyone (or even the majority) is happy, when the definition of "happy" is "much more than you could possibly get".
That's life, I guess.
The Commission is not instated by God Almighty or by hereditary laws: it is nominated by democratically-elected national governments. The Council does not spring fully-formed from the head of Zeus: it is made of democratically-elected governments. The European Court of Justice was not created by the Pope 1000 years ago: it was created by democratically-elected governments through treaties. And so on and so forth.
The fact that such governments are then able to sustain the fiction that they have no say in EU matters, is more a reflection of the poor state of critical thinking in voters across the continent than an indictment of EU's "democracy level", whatever that might mean... unless we assume that a process is democratic when it agrees with one's opinions, and completely tyrannical when it doesn't.