I had a major issue associated with this topic. I built my rating from 1100 to 1500 on 2D programs and 2D books (obviously), but then when I entered by first USCF tournament, I got beat easily by a 1230 and 1365 player. The 3D board and pieces had me very confused and disconnected from all of my acquired knowledge. I asked the more experienced players about my problem and they told me its very common. The problem, they said, is this:
"Strength in chess is all based on pattern recognition. As you develop your skills, you remember tactical patterns and positional patterns of the pieces that remind you how you should play. When you study 2D chess, you are learning about patterns that appear completely different on a 3D board, which renders most of your 2D knowledge as useless. A 2D board is perfectly flat with perfectly equal squares on all sides, with pieces that simply slide in cardinal directions. A 3D board changes shape with distance and contains pieces that pop out of the board and cause you to think about the logical connections in a different way."
After recieving this insight, I ditched all 2D forms of study. When using a book, I set up the position on my actual tournament board so the new patterns were learned in the same environment I would later compete in. On this website, I use the 3D option, but I still believe it to be inferior because the board is not 3D. Only the pieces are. Trust me, it makes a difference.
2d vs 3d chess
For those of us that starting playing a long while ago and are patterned on a physical board switching to screen study can be difficult. I had always done all my prep with at least one board, often two, and the first year I used only a PC for our state championship my result was my first train wreck since I was in high school! When I got to the event and starting playing my thinking felt FLAT really! looking over the board I felt adrift
of course since then I have had some other disasters, but that is just because I am older than dirt 
Will said a good point, for OTB it's somehow more practical (and implementable) to have a 3D board (meaning a real board) but scientifically speaking chess is a 2 dimensional game played on a plane! So adding a 3rd dimension only increases the complexity which is why I'm not a big fan of tall pieces and sets that don't have enough spacing. Personally I think I can see tactics better (and quicker) in 2D board than on a real chess board especially when many pieces are left on the board.
According to my observation 3D chess would be more exciting for game players as 3D game gives some extra effect to players. 3D game development has played an effective role in engaging more players.
You can follow this links to learn more about 3D game development services https://www.cubix.co/3d-game-development
3D board, in chessmaster with a big screen looks very close to otb.
In Fritz 13 because of the bad and slow GUI in Fritz I prefer 2D
on chess.com 2d
OTB 3D.