Sorry, I must have misunderstood. I assumed when you said residency you meant PGY2. You're probably right that it's not as simple as PGY2>MBA or vice versa, but as you mentioned, experience is second only to luck in helping land positions. I'd still think that experience gained during a PGY2 would trump the MBA most of the time, but I don't exactly have first hand experience with the issue either.
The "rare" factor of a management PGY2 would, if nothing else, differentiate your app from the rest of the stack I imagine. I'd rather be the candidate with something unique to offer, even though lacking an MBA might close some doors where it's a de facto requirement.
I don't even start pharmacy school until this fall though, so if you (or anyone else with experience) needs to straighten me out, feel free to do so