First of all, I would like to say that I love this game. I think it's the second best FF ever made (FFVII for #1), and there are plenty of GOOD ideas in this game. But I'm just going to talk about the bad ones.
I'll start at the top.
1) Pailings
There is nothing more frustrating in the world of video games than an invincible enemy. Nothing else can fill you with a feeling of helplessness quite like it. Sure, it doesn't last forever, but it destroys the progress you were making on a boss HP, and the sense of getting something accomplished while you were at it. The exact same effect could be achieved simply by tacking on more HP to the bosses, and it wouldn't leave you nearly as frustrated and irritated as the pailings do.
2) Identical License Boards
The License Board itself has pros and cons, but the fact that they are EXACTLY THE SAME for all the characters is definitely a bad idea. You have six characters who are all carbon copies of each other, no variance at all. Even in games such as FFIII and FFV where you had all characters able to choose any job had more variance than this game, because turning someone into a black mage meant their attack would suck. In this game, you slap a Masamune and mystic armor on a character and you have a character that can deal superior physical AND magical damage. Additionally, characters have access to all spells and all technicks at all times. In FFIII or V, turning someone into a black mage meant they didn't have the incredibly useful white magic spells, not so with this game. This removes a critical strategy element (role assignment) in a game that was already lacking thinking power.
3) The nature of secrets
Sure, the game is beatable at level 40 with Maximillians and Golden Axes, but to really experience all the game has to offer, you need to search for the best weapons, the best armors, etc. However, the methods by which you acquire these things are incredibly obscure with absolutely no in-game hints at how to get them. How is anyone supposed to figure out the Zodiac Spear on their own? How are you supposed to learn that by killing a billion necrophobes you can get a Danjuro? How is anyone supposed to figure out the Bazaar combinations for Tournesol on their own? That is, to say nothing of the Canopic Jar which only purpose is to help you get the Tournesol since Arcanas are only used in one other recipe an item that you can purchase straight up from a shop later in the game.
I'll start at the top.
1) Pailings
There is nothing more frustrating in the world of video games than an invincible enemy. Nothing else can fill you with a feeling of helplessness quite like it. Sure, it doesn't last forever, but it destroys the progress you were making on a boss HP, and the sense of getting something accomplished while you were at it. The exact same effect could be achieved simply by tacking on more HP to the bosses, and it wouldn't leave you nearly as frustrated and irritated as the pailings do.
2) Identical License Boards
The License Board itself has pros and cons, but the fact that they are EXACTLY THE SAME for all the characters is definitely a bad idea. You have six characters who are all carbon copies of each other, no variance at all. Even in games such as FFIII and FFV where you had all characters able to choose any job had more variance than this game, because turning someone into a black mage meant their attack would suck. In this game, you slap a Masamune and mystic armor on a character and you have a character that can deal superior physical AND magical damage. Additionally, characters have access to all spells and all technicks at all times. In FFIII or V, turning someone into a black mage meant they didn't have the incredibly useful white magic spells, not so with this game. This removes a critical strategy element (role assignment) in a game that was already lacking thinking power.
3) The nature of secrets
Sure, the game is beatable at level 40 with Maximillians and Golden Axes, but to really experience all the game has to offer, you need to search for the best weapons, the best armors, etc. However, the methods by which you acquire these things are incredibly obscure with absolutely no in-game hints at how to get them. How is anyone supposed to figure out the Zodiac Spear on their own? How are you supposed to learn that by killing a billion necrophobes you can get a Danjuro? How is anyone supposed to figure out the Bazaar combinations for Tournesol on their own? That is, to say nothing of the Canopic Jar which only purpose is to help you get the Tournesol since Arcanas are only used in one other recipe an item that you can purchase straight up from a shop later in the game.