Here are some quick reactions on how control might be improved, without understanding the limitations of the game's development.
The game pastes quicktime events over objects in the game as you near them to show you what you can do, and overall the approach seemed improved from Indigo Prophecy, but it was still often difficult to tell what action an abstract motion was correlated with. Am I drinking orange juice or closing the fridge? I don't know, even though my character would.
Descriptions appear with actions when they are thoughts around my head, so why not "Close," "O.J.," and "Beer" in the fridge interface? If screen real estate with multiple options is a problem, let me use the camera to "focus" on a particular icon and accompany that with text.
A system for hearing your own thoughts was an interesting convention that could have helped my personal knowledge of the world, but the mechanics of the system were occasionally vague when using the system was important. The game never explains that you sometimes need to think something near another character in order to make a branch of action appear. Also, there was a few times in the game where dialogue choices via thoughts appeared wherein either the selection or button was too difficult to read to make the choice I wanted within the timeframe given.
Visibility seems like a matter of tuning alone, but if actions become available after thinking something, then have related icons flash in the screen after you think them. For example, I think about feeding my son, and an icon flashes near him. I go over and talk. After our chat, icons flash in the kitchen near the objects I use to prepare dinner. A brief icon flash is way less of a immersion deal-breaker than playing a character that doesn't know how to feed his son a damned microwave dinner.
Driving Your Human
You are propelled forward in a walk by holding R2, and it sucks. The left analog stick is obviously more intuitive, and the character happened to move around like a tank anyway; very unresponsive controls.
If keeping it on a trigger is absolutely necessary, at least make it so that holding the trigger turns on a "ready-to-walk" mode (instead of "walking" mode) and then move in the direction you want with the stick. In avatar control, the animation really should compensate to player intent. If I want to change directions, make me move in that direction instantly, and let the system interpolate.
It was a shame control ever got in the way of immersion, and I would love to see these things addressed somehow, if another game like Heavy Rain is ever released. (I hope so!)