Banner is clearly smarter . Marvel make it a point of referencing him among their "great scientists" far more often than Ock . There have been storylines where he has dealt with specific threats better than Richards and co. He backs it up by building Anti-class 100 tech that work far more effectively than say Tony Stark's efforts with the same go . Ock's not built tech as anywhere near as consistently on a class 100 scale
Why are we here?
"Superboy Prime (the yelling guy if he needs clarification)..." - Postmania
"...dropping an orca whale made of fire on your enemies is a pretty strong opening move." - Nik
"Why throw punches when you can be making everyone around you sterile mutant corpses?" - Pendaran, regarding Dr. Fate
in a universe where radiation gives you super-powers instead of killing you this seems like a strange complaint.
even if you accept the absurd idea of a mind transfer is possible this wouldn't suddenly transform his personality. he's been 'evil' for a long, long time. if we transferred the Joker's mind into another body he wouldn't suddenly become a moral, upstanding member of society, would he? (some people have this idea that the incident that turned his skin white made him crazy... )
it would also depend on the era of stories we're talking about. Classic Otto actually seemed to learn from his mistakes and developed better plans as he moved along. before the Goblin came back from his amnesiac spell and killed Gwen he was actually second or third fiddle to Otto in terms of Spider-villains. Banner, well, I don't remember him as well... I always end up thinking of the Hulk instead.
Think of it more like a computer. If you accidentally magnetize part of the hard disk and somehow only corrupt your games folder, making a backup disk and using it to copy your OS to a new, unmagnetized, computer won't magically restore your games. That info is wiped out.
It does mean, however, that you could then install new games in that folder. Similarly, Doc Ock in a new brain wouldn't necessarily just 'be good' again, but he'd have the capacity to learn to be good again.
(Of course, actual brains cope with function loss fairly well - it just designates a new area of the brain to process the load. They had to relearn everything from scratch, but people have regained sight, language capacity, and motor skills lost to brain damage simply because their brain just started reallocating resources. Presumably Doc Ock could have learned to be a good guy again, even in his original body, but just never faced a compelling need to practice doing so.)
Nothing is set in stone.
I believe that it was the REASON Ock went over to the dark side. But he has been there for a loooong time.
In my own opinion, arguments could be made both ways and it would probably depend on the person. We're pretty complex things. One person might have this issue with his brain fixed and have a crisis of conscience. Another might have the issue fixed...and heck, that's the person they've become, why would they change?
Why are we here?
"Superboy Prime (the yelling guy if he needs clarification)..." - Postmania
"...dropping an orca whale made of fire on your enemies is a pretty strong opening move." - Nik
"Why throw punches when you can be making everyone around you sterile mutant corpses?" - Pendaran, regarding Dr. Fate
Given the ridiculousness of total mental transfer from one brain to another as an idea, it's kind of a moot point to argue semantics over whether or not effects originally resulting from brain damage would continue.
We're getting into comic book science logic.
One way to compare might be to look at what they have invented. Mere research or problem-solving capability is difficult to benchmark, but inventions are something tangible that we can evaluate.
Bruce:
1. Gamma bomb
2. Absorbatron - absorbs all the force of a nuclear bomb explosion
3. Orion missile - delivery system for a bomb payload, noteworthy because it could not be intercepted by other missiles once in flight
Otto:
1. The Mind Swap procedure
2. The Octavian Lens - a satellite network capable of either preventing global warming or making it worse
3. Octobots - a variety of octopus-themed robots, some of which he could control directly with his mind
4. The Harness - various versions of four metal tentacle arms attached to a harness
Based on inventions, I think that Otto wins this.