Yeah it was deliberate, but their origin in the first place was deliberately tied to Fantastic Four anyway, so it's not like some huge revelation. Besides the U-Foes are bad guys anyway. So it makes sense to have villains who are basically the anti-Fantastic Four fight the Avengers. I doubt it was some huge insult to the higher-ups or Fox. Sooner or later, these times with X-men and Fantastic Four will be over. Everything is going back to Marvel eventually. It may not happen a year or two years from now. But ultimately, that's what will happen.