The European Citizen has written an article on the need and possibility to reform the European Commission.
Without going too much into details, I would simply advocate a Commission that is completely detached from national considerations, because the tasks the Commissioners fulfil do not justify balance between member states but competence in their respective fields, as well as an ability to think in European dimensions and to lead a rather significant administration in a quite complex environment.
However, seeing the last eight years, I doubt that the EU is capable of substantive reform.
Its grown complexity with a perceived close-to-infinite number of veto points has become a heavy burden for this European tanker trying to navigate on the global sea.
Sure, we might see the Lisbon Treaty ratified soon, but this is not a revolutionary text, despite some obvious institutional and procedural changes. Under Lisbon, some dynamics will be changed, some equilibria will shift from one institution to another - largely depending on the practical interpretation and implementation of the Treaty's provisions.
Still, the true reform potential that would make the Union an effective and efficient democratic polity involving multi-level politics with a sensible mixture of representative democracy, administrative co-ordination, and involvement of citizens and socio-political interests concerned, is missing.
To make a long story short: Post-Lisbon, the EU won't see any substantial reform for a long time, no matter how urgent it would be. There are too many veto points built in the system, and these veto points mix the evils of individual high-handedness with the conservative force of big masses based upon non-rational logics that will always work against a reform that is felt and seen on the surface.
Only an external (or strong internal) shock might induce such a reform process, but in the end, its impact will hardly be sustainable long enough to put pressure on the Union for a sufficiently long time-period that would be needed to get a reform not only formulated but also ratified within 27 (or some more) member states.
Reforming the EU is impossible - and, yes, I know that prophecies can be self-fulfilling.