This is primarily the fault of national governments, for which BXL is a convenient scapegoat for their own mistakes, and secondarily of voters who ignored European elections for too long. Post-Lisbon, MEPs do have significant powers and ultimately designate the Commission President, so it does matter who you vote for AND that you vote at all.
For McCreevy in particular, the Irish government should shoulder a lot of the blame for nominating him, at a time when Commissioners were extremely powerful. These days a Commissioner so divisive would likely get shut down by EuroParliament. Also, I might be partisan but the last three Commissions were mostly a reflection of centre-right parties (EPP etc), which still command a majority in EuroParliament as well as in the Council. As long as people keep voting right-wing, we will get right-wing policies.
Like with all democracies, we get the politicians we deserve, not the ones we need.