Street Fighter x Tekken won't actually delete your saves. However, Ono joked in an interview with IGN that the only feature he could confirm for SFxT at this time was that when you install the game "all Bandai-Namco save data will be erased."
Another revelation from this interview was that the two crossover games are not based on SF4 and T6, respectively. They are also not the sequels to those games. The "Cross" games will be all-new products drawing from the entire Street Fighter and Tekken series. Harada said, "I'm sure the graphical look of the game might change and the gameplay elements... will be quite different."
Also, Ono stated that his goal of having his game out in two years was heavily criticized by his boss, Keiji Inafune. Because of this, he will try to have the game out sooner.