If what Team ICO are doing is to essentially creating a controller setup to cater to their own audience, it doesn't make the design better. it makes it worst. That's objectively true, if you agree that a game is designed to be enjoyed by everyone.
If what they made is justified in the game design, then it's good design. For example, if having a more precise control is something that'll enhance the gameplay, it's perfectly reasonable. Skate is one example of games that decided to try something new to enhance the gameplay. Everyone agreed that it felt odd, but it only made the game more precise, better and fun. Dark Souls, too.
But you have to understand that it might not please everyone, and that if it doesn't, it makes it objectively bad, as the its intended design doesn't work.