Julien Frisch's recent article on Scottish Representation in the EP (in English; auf Deutsch) shows that, while the proportion of citizens to MEPs is the same in Scotland as elsewhere in the UK (except perhaps NI?), Scotland is underrepresented in comparison to small states of a similar population size such as Finland, which has 14 MEPs - more than double Scotland's share with 6 MEPs.
An independent Scotland within the EU would have more representation in both the Council and the EP, though I doubt that Scotland would get 14 MEPs in this scenario - most likely that the number of seats for other states would go down to fit in with the current cap of EP seats (736 is it?). Under Lisbon a similar system applies with the seat cap at 751 MEPs.
Grahnlaw responded with a post about the representation of citizens in the EP, which are based on degressive proportionality - small states are over-represented to the extent that the weight of your vote varies wildly depending on which country you are in. So if you live in Malta or Luxembourg, your vote counts more than that of a citizen in Germany.
Grahnlaw is right that this is all about representing the states rather than about finding a way of representing the citizens on the one citizen, one vote model. It is probably also true that with the system set up this way it will be almost impossible to reform it into line with this model. However, since the EU is primarily an Union of states rather than of peoples, I can't see much of an alternative to the way it started except a radical straight-to-federation Union, which still isn't politically possible.
That representation is tied up with representation in the Council makes the whole thing more complicated, but I don't think the fact that the two are linked is in itself bad or irrational. It's part of the debate in any federal or quasi-federal structure: what should be the representational balance between big and small states, and how should citizens be represented? My personal feeling is that there should be a minimum representation for states in the EP: national and state identity matter very much, and, though the Council is the proper place for national representation, there should not be the sense that small countries are being pushed out of the EP, which is one of, if not the, most legitimate institutions of the Union.
It would not be good if the people of small states became less trusting of the EP, and felt that it didn't represent them.
That said, "the one citizen one vote" argument is powerful, and needs to be addressed - here, I would say that as states become more equal in the Council (of course, veto thresholds would need to be raised), seats in the EP should be distributed more fairly, with the minimum allowance for MEPs per state cut down - e.g. to 2 per state. After all, if states' votes in the Council were less weighted according to population, then it would be more logical to make EP seat distribution more fair.
I should note that an important question here is one of identity, and of national representation versus individual representation - which is linked to ideas of national versus individual sovereignty, which I've mused about here and here. Since I come down so much on the side of individual sovereignty in my mini series so far, it might be surprising that I've stressed the need for some recognition of national identity in the EP. While I wanted to show with my first two posts that it is a mistake to nationalise notions of sovereignty and legitimacy (and that there can be adverse effects to concentrating these concepts into one identity), I still think that national identity is of great value - just that it shouldn't be of paramount value. Identities do matter in representation, and this should be allowed for in the EP and the overall EU structure (just not in the overpowering way it is now - I agree that citizens should be the most important group, rather than states).
And then, of course, representation in the Commission is another queston...
Edit: I've posted a few more follow up comments here. Sorry to divide things up like this.