In parliament, they get the most MEPs because they have the largest populations. In fact, one could argue that they have proportionally less representation than the smallest members, since the minimum number of MEPs per country is 6. For instance, Germany, with a population of around 81 million, gets just under 100 MEPs, while the least populous can get 6 MEPs with a population of around 500k.
In the council, all countries have equal representation, because every member state sends their head of government, and similarly for the various councils of ministers. The president of the commission is elected by the parliament along European political blocs, and the current president is from one of the smallest EU member states (both in terms of land mass and population). Commissioners are distributed more or less evenly between the member states, and there's no guarantee the most important commissions will go to the largest member states.