Just like Maltese have around 10X the voice of Germans in the European Parliament.
In the US, each state has 2 votes in Senate, representing the rights of the states to govern themselves as independent entities in many things. In the EU Council has one representative from each member country, representing the right of those countries to govern themselves in many things. Both reflect that each member state has a different history and culture, may have different levels of taxation and varied policies toward the common good, and to some degree may have differing laws even though most of them are shared.
In the US, each state has proportional seats in the House of Representatives, based on the population of the states. It's step function, since you can't have partial representatives, but it's pretty close. In the EU Parliament, it's a degressive representation - smaller countries have more representatives per capita than larger countries.
In the US, the electoral votes for President are distributed based on the aggregate number of Senate and House seats. Smaller states end up with a slightly higher vote per capita, because the 2 Senate seats are spread over a smaller populace. But they're relatively close to population.
You're complaining about Wyoming having 3.5X the power of CA in the election. Malta has more than 10X the power of Germany in EU.
Do you think it would make sense for Malta to end up permanently governed at the whim of Germany in the EU? Do you think that Germany would act in the interest of the citizens of Malta? Do you believe that because Germany has more people and is bigger, they should be allowed to dictate EU policy without consideration for the differing culture, national policies, and histories of the other member countries? Would that seem fair to you?