If a cleric chose to follow a deity whose favored weapon was the bastard sword, would that cleric gain "Martial Weapon Proficiency: Bastard Sword" or “Exotic Weapon Proficiency: Bastard Sword"?
I'm inclined to think the latter, but I not certain.
As a DM I would be inclined to say both based on the wording of the Cleric proficiencies: "Clerics are also proficient with the favored weapon of their deity".
Quite simply you are proficient in the weapon, no matter how you use it.
On the other hand, for balance you could make a decision based on how the deity "favors" the weapon, do they use it one-handed or two-handed? or you could have the cleric choose one.
I would say Martial, but jeez, good question. Who has Bastard Sword as prefered, anyway?
After a quick perusal of my books, it seems that the Forgotten Realms has the most deities with Bastard Sword as their Favored weapon:
Ragathiel (an Empyreal Lord)