Would you suggest giving Bulgaria a seat at say, the UN Security Council?
Do we deny Scottish MPs a vote on defence matters? What about prime ministers being from different parts of the UK, which in economic output and population are not equal? Should an MP from London hold greater powers than an MP from Yorkshire and Humber?
It's a bit of a tangent but: Bulgaria already held the rotating seat for Eastern Europe three times, iirc. And sure enough, for the benefit of world peace and stability, there's good reason to enlarge the number of permanent seats on the UNSC and make it more representative. Unless of course you subscribe to might is right, or believe that certain states should have preferential treatment on historical/nebulous prestige grounds. Though under these terms, however powerful one initially is, one ends up screwed eventually, with no legal recourse to turn to.
But it's apples and oranges: the EU and the UN are different organisations, with some overlapping history. Indeed, the former has proven far more effective at putting its jointly agreed resolutions into action on the ground; and defence is a subsidiary matter for member states as well, so again, there's no direct analogue between the UNSC and the security and defence cooperation in the EU specifically in terms of protocol.
And, yes, I'm well aware that one can find bias and disparity in international law and systems; it is not perfect; but this does not mean that the ideal of equality before the law should be chucked out of the window at the first sign of administrative difficulty, historical flux or pressure from extremists. That is of course if a more representative, democratic and accountable institution is the end goal.