If I assume that Benfica and Napoli will face each other at the semi final which can happen I think that between these two teams it is only natural for Napoli to come out victorious because of their awesome performance during all the season in Serie A and in Champions League.Benfica had somewhat of a same season but I think the difference in Serie A and Liga Portugal is still notable despite Serie A losing value each year that we pass.For me personally though I predict Inter to be in the semi-finals and I have no prediction of which other team will be here.
Benfica look to be a good team and they did performed well in Champions League but I don't think they can easily beat Inter Milan. Between them and Inter Milan does not have big quality difference and they can beat Inter Milan but chance is like a little bit fluctuating around 50%, a bit lower or a bit higher than 50%.
Even Napoli will not surely beat AC Milan even they totally dominate Serie A in this season. However, in knock out matches, one mistake or one fantastic moment from a star player can decide winner. At this stage, all clubs have star players who can make such fantastic moment and we can not know what players will make it. Time will tell and we will know the winners after ending of quarter final stage.
I agree that having semi finals between two clubs from two domestic leagues would be more exciting than an internal meeting.