One idea could be that Frieza and Goku are forced to team up against a new, even more powerful enemy. They start off hating each other but gradually learn to respect each other's skills.
Another plot could be that Frieza, in an attempt to get stronger, makes a deal with Goku. Goku agrees to train Frieza in exchange for Frieza's knowledge of some ancient and powerful techniques. Along the way, they have to face many challenges both from within (like their own pride and distrust) and from outside forces that don't want to see them work together.
Perhaps in a different universe, Frieza is redeemed and he and Goku become friends. They could train together and combine their powers in new and unexpected ways. For example, Frieza's unique combat techniques could be merged with Goku's Super Saiyan forms to create a whole new fighting style.