It's a fairly made and properly executed system that I find no fault with.
It has problems now, but once the initial rush dies down, it will be fine.
Being the champion is based more on luck of having a decent monster early on than skill.
There are too few match slots relative to the popularity.
The application system is crap and only encourages third party tool use.
The system needs a way to prevent monsters below a certain level from clogging the applications.
Too many people are only using this to powerlevel their monsters, since you're guaranteed 100 experience here and the other pits are almost always mismatched.
The champion system is flawed because without being the champion, it takes weeks to get high enough to even compete.
With no rewards besides "bragging rights" for being the long running champion, it's unfair to keep a level 50 monster in that nobody else can even touch in at this time.
All of the above (minus first and/or second options).