From the IMDB:

Putting the Alien (1979) skull on the trophy case on the Predator ship was the idea of Stephen Hopkins' as a way of showing off all the different species and creatures that the Predators have hunted and killed. It was also a nod to the Dark Horse Aliens vs Predator comics which were quite popular at the time. Since Fox had owned the Alien film series, it was easy to obtain the rights to use the Alien head in the film. This excelled popularity of the Aliens vs. Predator series crossover throughout the 1990s, and was promptly followed by more comic books, novels, video games, toys, and eventually movies.

Alien and Predator comics were published from around 1989, but The "Alien vs Predator" wasn't published till February 1990, same year as the Predator 2 movie. So in other words the movie is a nod to the comics but I really doubt that there were serious plans to make an "AvP" movie then.

From the IMDb:

Putting the Alien (1979) skull on the trophy case on the Predator ship was the idea of Stephen Hopkins' as a way of showing off all the different species and creatures that the Predators have hunted and killed. It was also a nod to the Dark Horse Aliens vs Predator comics which were quite popular at the time. Since Fox had owned the Alien film series, it was easy to obtain the rights to use the Alien head in the film. This excelled popularity of the Aliens vs. Predator series crossover throughout the 1990s, and was promptly followed by more comic books, novels, video games, toys, and eventually movies.

Alien and Predator comics were published from around 1989, but The "Alien vs Predator" wasn't published till February 1990, same year as the Predator 2 movie. So in other words the movie is a nod to the comics but I really doubt that there were serious plans to make an "AvP" movie then.