You are one good example of why academy exists.
I only play Arena and when you read through the forum most of the users prefer it as well. The only negative experience I sometimes find myself in are very long games.
As I understand it academy was created as an introduction to mage wars. A version that was easier to learn and to understand and that provides a quicker gameplay. Beginners sometimes are scared by 3 hour games with tons of rules.
I guess Arcane Wonders wants more people to play mage wars in general and with academy they reach the beginners. That is why they focus on it.
(But as my opinion Academy is quite complicated. Cards made for academy with different ruling for arena mages and the slightly different core-mechanics between both variants makes this worse)
Summary: arena is and will be great and academy will add more and more cards to arena, making it even better!
Welcome to this awesome game arena