Tobi has the rinnigan..and had enough time to think when naruto was about to hit him with that rasengan, why didn't he simply absorb it? Did he forget he has that move? We all saw madara do it in mid air being tossed around.
It simple really, when tobi is using the sharingan, he can't use the rinnegan and it takes time to absorb and one more thing they have shown it before when he was controlling the tail beastss so pay attention more.
Naruto got to him way too fast for him to react. People don't remember how fast Naruto is, If Tobi just about realised he was there, he won't have the time to use a technique.