I definitely prefer CommandBased because of having commands and subsystems split out into separate files. Yes, managing all the files can be a little hard and the structure can get confusing (most of the time it's me going "wait, did I declare that in
this subsystem or
that one??") but overall, it keeps everything clean and spread out so that if you break something it's easier to fix.
Not sure if you've read it, but this is the reading the previous head of programming had me read that inspired the use of the CommandBased robot:
http://www.laputan.org/mud/ It's an interesting read, I suggest you take a look.