Why so many people have problems with the junction system?

I feel that is an easy and intuitive process. Played it as a kid, and just saw it as "Oh, I can link my magic to boosts my stats, the more powerful the magic, the more powerful the boost, and also some magic works better for some stats (like healing magic being better for hp)". But I see that the main complain with the game is that system, and I really don't understand why.