All sides can lament, but the numbers speak for themselves.
'The apportionment of seats is not proportional to each state's population, nor does it reflect any particular mathematical formula; however, it is stated in the treaties that distribution of seats should be "degressively proportional" to the population of the member states. The process can be compared to the composition of the electoral college used to elect the President of the United States of America in that, pro rata, the smaller state received more places in the electoral college than the more populous states.'
https://en.wikipedia.org/wiki/Apportionment_in_the_European_...
There's the EC and bureaucratic ad-hoc groups that nobody appointed like the Eurogroup (an informal assembly of eurozone fin-mins with super powers that's not legitimized anywhere officially), the council of the EU (composed by state leaders and making decisions where strong countries like Germany and France have disproportionate influence using lackey satellite countries or debtors they control), etc.
Here's another Wikipedia link for you:
https://en.wikipedia.org/wiki/Democratic_deficit_in_the_Euro...
The opposite is usually lamented in the heavier countries, e.g. here in Germany it is often lamented that a German voters vote is less important than that of a voter in a small country like Luxembourg due to the way EU representation is structured.
Additionally, the voting process in the European council is structured so that bigger countries cannot just impose their will in smaller ones (see https://en.wikipedia.org/wiki/Voting_in_the_Council_of_the_E... for details).