I would say that it depends on the application. When I had my 18 footer i simply did not have the room to run a mast system and I ran Church Walleye boards all the time. But the bigger boats I have owned, I have stuck with a mast system. Some guys just simply prefer one over the other. They both work but they both do the job differently.
Inline boards are extremely versatile. The walleye guys have showed how versatile they can be by running multiple leadcores and snap weights per side. The Michigan guys latched on to this and have adopted the inline boards to run 3, 4, 5 coppers per side. No matter if you are trolling for spring browns or pulling a 500' copper, they can do it all. IMO, if you are looking, Offshore and Church both make great inline boards.
pros
versatility (copper, cores, mono, braid, snap weights, divers)
inexpensive vs mast system
ability to run multiple sinking line presentations per side
cons
fight the board not the fish
tough in rough weather (boards tend to dive)
a bit more complex to operate
I run big boards 99.9999% of the time. They are in the water every day and they spend the entire season in the water. Spring, summer, and fall. I use them for flatlining in spring, pulling short cores, pulling copper. They work for me for everything I do. I run Big Jon Otter boats (double keels) with 200# power pro. Amish outfitter planer board releases for spring flatlining (mono) and Scotty planer board releases for everything else (copper, cores, etc). My planer reels and pulleys are mounted high on the hard top which provide a hard downward angle to the water. This keeps the planer line out of the water and also helps releases slide down the line nicely. This system with this stuff in it works great and Im having trouble improving on it.
I have fished with big boards that dont "pull" right, or the planer board line spend most of the time in the water, or releases wont slide down or boat full of bad releases. The reason I mention the details is because a poorly setup big board/mast system can be pain staking, frustrating, and hardly worth the effort.
pros
releases allow you to fight the fish not the board
pull hard to the side and stay out of the way
very simple to use
cons
big investment
lots of components
storage- big boards take up lots of space
almost impossible to run more than 2 different presentations per side (multiple coppers, cores, snap weights, etc)