That still doesn't make it a prequel, it is the first part of a series that takes the material it is adapting and presents some of the events in chronological order.
I think prequels generally don't work because they are too boxed in. It seems when people make prequels it is felt that they should address every little thing. X-Men First Class is one of the best prequels I've seen, but it still suffers from this. (FIRST CLASS SPOILERS FOLLOW) By the end of the film Xavier is in a wheel chair, Magneto decides to be a bad guy, and Mystique decides to leave her long time best friend Charles to go be bad with Magneto. All the chess pieces are lined up in their exact places for the first X-Men movie, even though it takes place a very long stretch of time later. It feels like many of those elements were forced in there because well, obviously these things have happen to the characters sometime.
Much like Padme dying, the Death Star being built, and Anakin donning the leather suit in ROTS. There was no rule saying that those things had to happen in the prequels, and I'd argue that they really didn't need to (at least not if those events were of no more importance to the story that they could afford to be shoved into the last 10 minutes of a nearly 7 hr. long trilogy). 20 years pass between the trilogies, but yet all the pieces are in place for A New Hope, Luke, the droids, Yoda, we find these characters just where we left them.
At the end of Star Wars they are in this fancy Mayan Massi (or something) temple on a nice sunny forest planet, Empire Strikes Back comes out and suddenly they are in the snow. Were our minds blown? How did they get there!!! What is going on???!!! Nope. If these movies were made today and Star Wars was a prequel to The Empire Strikes Back, you can bet it would end with the crew arriving on Hoth.
A story needs to be focused primarily on character and plot. To me, X-Men: First Class was good (despite the awful title) because it did focus on characters and had an interesting plot (well, the Sebastian Shaw/Magneto stuff was great, teenage X-Men stuff was painful at times though). To me, the parts where it failed were the parts where they felt they were obligated to showing us things we already know must happen sometime just for the mundane sake of showing us. A character becoming paralyzed from the waist down could be some powerful character development for a potential later film, or it could just be shoved in at the end of the film with a nudge and a wink, "Hey, look what just happened! Ha, and now you know why he is in a wheel chair! Always wanted to know that didn'cha!"