A common misconception. Just because Obito is scared of Itachi, does not mean that he is weaker than him.
If anything, Obito was cautious of Itachi's abilities as he was a thorn in his side, however note that Obito was still confident enough that he could dispose of him - note "IF Itachi knew my secrets, i'd be dead".
I'm not a fan of the "Itachi's intelligence" response. In fact I don't really like using intelligence that much in arguments at all. It's far too empty. Firstly, just because Itachi's shown to have good analytical skills, does not mean we can automatically assume that he has a solution to EVERY SINGLE PROBLEM he's faced with during a battle. Secondly, don't think that Itachi's the only one in Narutoverse that holds the title of "The Man with The Plan". Remember, Obito has done the following:
1. Taken control of the Akatsuki
2. Manipulated members of the Akatsuki to his will behind the shadows
3. Took on the persona of Madara Uchiha, a secret that would have been kept had Kabuto not summoned Madara.
My opinion:
MS Obito vs Itachi? - Close, but Obito wins
MS + Rinnegan Obito vs Itachi? - Obito wins fairly easily
I know that Itachi's cool and everything but every good character has his weak points. I don't think he can beat Obito. Or Kabuto for that matter. But that's a different story....