I always seem to be the person who sits on the fence with these sorts of threads...
I took a long break from RE2 after my first run playing Leon A/Claire B, partly due to Kingdom Hearts III being out at the same time and also due to general busy-ness. However, I've got back into the game this week and I like both scenarios equally for different reasons.
In terms of story, Leon's generally seems to have more in terms of the investigation into the virus and the outbreak itself, and his naivety really comes through, which I like because I feel like it's realistic - a person of his age going into that situation wouldn't know what was going on or who to believe.
However, Claire's scenario has the focus on protectiveness, compassion and how family should behave. I like her fierce protectiveness over Sherry when Annette doesn't display that behaviour.
I prefer both A scenarios to the B scenarios. I just wish is that they swapped over what happened in the scenarios the second time round, for example, Leon encounters Sherry in the B scenario and Claire encounters Ada, Ben and Kendo. It would have been interesting to see the reactions of each main character to the different scenarios.