They used the same complaint that I've heard over and over and never really understood...
"It was too different - and too confusing - for most people, who ended up relying on the overpowered Summon monsters, which had overly long, unskippable cut scenes."
The system in FFVIII was tricky, but rewarding. If you can't use it well you have the easier option of using summoning, but that takes longer as a result. What do people who complain about this want? Extremely cheap and powerful summons that can be used quickly so as to completely undermine any point to actually developing skill? Or would they have preferred no summons and just the complex junction system so that beginners were forced to try and use it?