It's an interesting point, and I suppose one that, with time, will evolve as the European Union continues to improve how it functions. I certainly think that more should be made of the groupings, and the public should be much more aware of what, say, the ALDE and EPP stand for and debate in the European Parliament.
However, whether it is best to take away the link to national parties I am not so sure. There could be an argument that says that would remove the EU Parliament from having any direct links to the people - as they would be entirely their own structure. It would certainly be a big step. Also, there is no set method of voting on MEPs as far as I'm aware - different countries vote differently. So that would also need to be sorted.