SSJ4 was intended to be in DBZ? I don't see how that can be a Funimation mistake, as I'm pretty sure Toei didn't have it in DBZ either. I seriously thought SSJ4 was nothing more than a GT invention. Tell me more! I feel ignorant...
Anyway, the most logical reasons for not having SSJ4:
Originally, there was a statement saying that a lot of the team hadn't seen GT. I don't know if this accurate now, but if it is, that's a pretty big hinderance.
A lot of people don't like GT. At all. Sure, it has it's fans, but the fans of GT are generally less enthusiastic than the anti-fans are unenthusiastic. Or something.
Finally, DBZ has <i>plenty</i> of stuff to put in a game without resorting to the 'sequel'. Seriously. Besides, it would completely unbalance the Saiyans, as there simply isn't another transformation for the other characters. (Frieza More Than Final Form? Really Really Perfect Cell? Fused With Lots Of Nameks Piccolo?) Three levels of Super Saiyan is enough. Anything more is just overdoing it.