@MelanieS, I've never been to Chefchaouen so can't tell you about it - not sure what the attraction is there. Without ever having been there, my impression from guidebooks has been that what "Chef" has going for it is that it is "not Tangiers" and is at least away from the worst of the ferry ports, which tend to be grotesque, made-for-tourists traps. I think it's somewhat popular because it's an authentic Moroccan town, rather than "the Tijuana or Morocco." It may actually be quite nice, or it might just be an average Moroccan small city.
That said, I'm quite confident that Chefchaouen would pale by comparison to either Fes or Marrakech, both of which are magnificent. There are plenty of cheap flight options to/from places around Europe from both of these two stunning old cities. I can't imagine that I'd trade a day in either of them for a day in Chefchaouen.
So my advice would not be to skip Marrakech - it's like no place else on Earth. Same is true for Fes. Chefchaouen...I can't say but I'd highly doubt it's remotely in the same league. If you have to pick two places, it would be no contest for me.
On a European trip where you want to include a foray into Morocco, it's a wonderful (and unexpected) way you can "connect" two cities in Europe by using the Marrakech-Fes train line as your "bridge." Fly from Europe to Marrakech, take the train to Fes (or do them in the opposite order), then fly from there to your next destination in Europe. Last time I did this, I flew Madrid to Marrakech, train to Fes, flew back Fes to Paris. It worked out perfectly. If you're trying to connect Lisbon and somewhere in Spain, I'd imagine you could do something similar.
