I have to completely disagree about Tony Todd being cast wrong there. My opinion may be biased, but here's why.
Back in 2006 (my first DragonCon), he was one of the first actors I got to meet. Truly a wonderful man to talk to... he's actually bigger in real life than on screen, if you can imagine that. Big guy, big heart. We talked for probably close to a half hour. He shared a personal story about himself and why he accepted that role. I always loved the episode and it makes me cry every single time I rewatch, but hearing his story made me appreciate what he did in "THE VISITOR" even more so.
Back on topic, I have a controversial opinion...
In some ways, based on "BEFORE AND AFTER", Chakotay would have made a better captain. Specifically, two things come to mind.
First, promotions. Tuvok, Paris, and Kim were all promoted. Chakotay seemed to understand that despite them being decades from Starfleet, it still means something to people aboard that their good work gets recognized.
Second, according to dialogue from Linnis, there are doctors, plural, on board. From the beginning, there should have been training of more medical personnel on the ship. Besides the obvious need of variety for different missions, if The Doctor was damaged or destroyed, they would be screwed, medically. Clearly, Chakotay understood this very practical necessity. Even THE WALKING DEAD understood the need to have doctors train other people to be doctors.