I see your point, but consider this: Every time he has entered the "dreamscape" he has either been asleep and Lisa has forced herself into it to spend time with him or he has been in a hightended state of mental distress. This stress showed itself as "corruption" earlier in the game among other things. It also showed itself when/if he confronted Spyder, where he gets to a point were he simply faints, but still manages to shoot off a small round of energy in his direction (this also happens in other places and other path, so I hope you get the picture).
As his Focus increases so will his ability to stand against said mental distress and thus he will eventually learn to control his growing power and make use of them without any consequences - or so it would seem
Also consider that our MC starts out with being an insecure, low selfesteem no sexual experience kind of guy. Maybe a strerotype, but not all stereotypes are bad. Stereotypes helps us to quickly relate to a person and even help us grasp an understanding of how he/she reacts or is expected to react, but the interesting "stereotype" is the one that at some point breaks the known formular and sort of moves into uncharted territory, where the reader is suddenly not able to predict said persons reactions and/or even motivations.
I did consider splitting this into more than just one path for our MC to explore. I even mapped out some of how they would diverge and ultimately lead to very different experiences and endings. Having a talk with a good friend of mine about this made me realize that it would be practically impossible as I'm only one person making this and any other path would basically become a whole story in and of itself, so I decided against it. Just to, as he pointed out to me: KISS (Keep It Simple, Stupid).
That is what I'm trying here, and yes I realize that we may not be operating along the same definition when it comes to the term "simple", this, to me, is a fairly simple storyline. The implementation is the hard part
About Nat, and I think I'll just end the whole Nat debate here (at least on my part) consider the following: When she feels so deeply betrayed she ends up at the bar meeting the only person who has helped her out in the past in this new and unfamiliar place (and Spyder goes by the name of Charles when he is at work of course). She downs a few drinks and they get to talking. He is quite understanding and offers to help her out by giving her a place to stay for the time being.
Every time she then meets our MC her reactions are not really aimed toward him, but he does become a proxy for the one she is angry with. Thus he becomes someone she can vent her frustration and anger at.
Anyways, this became far longer than I anticipated and went deeper than it should have about motivations and such and I'll just leave it at that or I might talk myself into spoiler territory in the future. So, no more about Nat from me
I'll go grab some more shut-eye. I think I need that.
Cheers - Kaffekop