You can pause the game in TB combat, too. The difference is it's non interactive.
In TB, there's a different metaphysic. The narrative doesn't explain that. Inconsistency. Hence, problem.
Pausing, going to your Settings menu (which also pauses the game), selecting something in your inventory (also pauses), a dialogue system (pauses) -- these are all normal gaming interfaces for the player to control things. Aside from dialogue, they are not part of the narrative.
Showing a character in a level in real time exploration, and then showing that same character in the same level in turn based combat, is the problem. Both Exploration and Combat are part of the narrative.
Learning how to exploit a game system is learning how to beat a game. We could say the same of min/maxing in any RPG rule set.
A spiritual sequel should improve it: but that doesn't mean replacing anything. Plenty of people were expecting the same type of game play from P:T. If it's not broken, don't fix it.
Combat is avoidable in P:T...so? I've never avoided combat. I wanted TNO to be in combat, to see what he and his party could do. He was one of the most powerful humans in existence, and his incarnations spanned the ages. Near the end of the game his END healing was akin to Wolverine. He was more of a force than a person at that point. What would be the point of having an inventory screen, and stats, and spells, if you're not going to see them in action? And why would a player run away from 10 bats or so? Is TNO scared of bats? Or gods, or his mortality for that matter?
Combat was part of the game, even if a minor point. And it had problems. But it didn't need to be replaced just because Mr. Cook had a new setting and rule set