Say what? Spiderman and X-Men have always been in the "same" universe. I'm not sure when the concept of "introducing" heros in other comics started, but back when I was a wee lad in the 80's, you definitely saw them together (in the aforementioned Secret Wars and in Marvel Team-Ups).
The Avengers, FF, Spiderman, etc. have all occupied the same universe. Heck, Beast was an Avenger for quite some time (as was Quicksilver and Scarlet Witch, both mutants). Spiderman and FF partnered together. Spidey's apparently a member of the New Avengers now. X-Men and Avengers and FF have partnered and fought each other at various time. There were no "separate universes".
In fact, right now I believe, there's some storyline about mutants having to register with the government and various superheros taking sides (like Capt. America disagreeing and going into hiding or whatever).