I know I've just posted on the allocation of EP seats among the member states, but I've had a few more thoughts - I was probably thinking too much inside the box (or nation state), and there are a few other ways of looking at the EP seating arrangements.
1. Have purely European constituencies. Instead of allocating seats on a national basis, distribute them on a European basis. I would be personally against this, due to my feelings on the importance of national identity (smaller states wouldn't wnat to be "divided up" while larger states would undoubtedly have several constituencies within their national borders). This could be changed to include 2 "national" seats per state.
2. Have a certain number of transborder constituencies. It would be limited to crossing the borders of 2 countries, or 3 at the most, due to language barriers. Otherwise seats remain allocated nationally.
3. Have some seats resevred for transnational lists. The seats of the EP could be "topped up" with voting for one of the EP groups, as well as "national" seats. The groups could pick the candidates for these lists themselves, rather than the national parties, so this would strengthen the party groups.
4. A mix of 2 and 3.
These options could have the effect of strengthening European-level democracy by giving the elections more of a transnational character structurally, leading to an incentive for a more "European" debate. There are probably more ways of looking at this, and I'd be interested to know people's opinions on this.