I think Thomas' chapters are actually my favorite.
I love Hugo and thoroughly enjoy playing as him but there is something about playing with Thomas that feels extra rewarding.
I mean you start out with nothing but if you take your time and do it right you can build the castle and the small group of people you can recruit up to be equally as good as the three main heroes and their parties.
That requires a lot of grinding through battle after battle though and I understand a lot of people don't have the patience for that especially after playing with higher level people with good gear for most of the game.
Still it is a challenge albeit an incredibly rewarding one and well worth the investment whether you rush through just for story or take the time to make Thomas great.