It would be more difficult for two people to sneak into the Senate Chamber. Not only that, Obi-Wan probably would have been more distracting to the fight than anything because Yoda would have to save his ass constantly, just like he had to do in AOTC from Count Dooku.
Also recall earlier how quickly the three Jedi who accompanied Mace Windu to arrest Palpatine got slaughtered. Obi-Wan would have provided no benefit to confronting Palpatine.