I can understand that if your goal is just to unlock all scenes as quickly as possible then those limits would be frustrating, but if you want to actually play the game in a way that makes the MC a reasonably consistent character whose choices have consequences for the world around him as well as himself, those limits are surely a necessary part of the process.
The DIK/CHICK system is meant to be an approximation of mood and personality. It is far from perfect, of course, and can't ever hope to convey the complexities of a real person's attitude. But there is a logic to the idea that a character who makes certain choices would lean in a certain direction, personality-wise, and respond to situations accordingly, that such a character would be more or less attractive to other characters as a result, and that the choices he makes would open some doors and close others.
If you're reading the situations and the dialogue and thinking about the choices, then some of the limits mentioned above shouldn't be coming as a surprise, in my view, because they mostly make sense within the framework of the game and the personality you've shaped for the MC with choices. A CHICK MC is less likely to want to respond to a situation aggressively, a DIK MC is less likely to want to hug a friend. Of course, we know real people are more complicated than that, but as a rough sketch it's not so unrealistic. I also don't think the choice about whether to go with Jill or take care of Sage is such a far-fetched dilemma the way it's presented, and the consequences of that choice seem about right to me, knowing what we know about Jill's personality in particular.
Each to their own, and mods can certainly have value sometimes, but I get a lot of satisfaction out of knowing the game takes note of my choices and unfolds differently because of them.
