First, remember that this is a travel forum, not an expat forum. The experience of visiting a place for a few days is VERY different from the experience of living in a place for months.
Second, I don't think you can make a "wrong" choice. It's all good. And while Madrid is indeed much bigger, Seville is hardly some tiny village.
Third, how you feel about the city will only be part of the experience. There's also who you meet, who your professors are, what course you take, etc. And that can't be predicted in advance so easily. If a college experience were only about location, no one would go to some of the small colleges in small towns in the US not near any "attractions" (I won't mention names to avoid offending) - and no one would enjoy the experience. Yet they do go and do enjoy it.
One big difference will be transportation. Madrid, being both the capital and in the geographic center of the country, has great transit links (by bus, train, or air) to the whole country. Seville won't have as many options, and for some places you may have to go through Madrid. If you want to see where you can go nonstop from Seville's airport, here's the Wikipedia listing: https://en.wikipedia.org/wiki/Seville_Airport#Airlines_and_destinations. I see that Ryanair has flights to a variety of places outside Spain; just be sure when using them, you read and understand ALL their rules FULLY, or you will pay a lot extra.
I'd go for one semester in each, particularly since the experience of each will be different, and since you don't know how you'll feel about each one until you're there.
Think of it in reverse. If a Spaniard said "I can spend two college semesters in New York, two in Denver, or one in each," and didn't give you any other details, what would you advise? Of course, I'm not making exact equivalences in cities, but you get the idea.
