I do theories for fun, including one that was posted here in another thread, but what I really believe is that Madotsuki's room is not the only one in her apartment. There might be something else behind that door, but we can't see because she won't get out. I can't see the Toriningen as bad creatures, but I'm not able to explain why they are good, either.
There is a very easy explanation for Poniko. You know when you see creepy things in the dark that aren't actually like that, right? Madotsuki could have gone to her house once, and saw a disturbing face somewhere in the room while the lights were off. My friend is disturbed by Uboa's face and sees him in random places in the dark, and she never played the game.
And I actually think almost all of her dream creatures represent someone she knew in real life. Not necessarily died, because almost all theories say Madotsuki's friends died... Actually, they don't even need to LOOK like that in real life. Monoe would be a girl who would always leave when Mado tried to talk to her, for example. Also, Monoko could have never had five arms IRL, It's just the way Mado recreated her in dreamland. Maybe she thought Monoko was ugly? Haha.
Shitai might be an adult/older friend who left for somewhere very far from her and didn't come back, and she translates it into her dreams as him being dead. Other colored people (there are some in the Mall and the sky garden, right? the green on Shitai doesn't exacty mean OMGDEAD, since there is another green guy in the Mall) could be other friends of her who left, or older friends.
I actually like the theory that Kyukyu was from a cartoon show Madotsuki liked. One day she went to watch her cartoon, and found out it was replaced with something boring or scary.
Mafuraako would be a very shy person, Mafuraako would be a girl who was always sleepy, maybe not always SLEEPING, but well, that's Madotsuki's interpretations in the first place. She saw her as a girl who would sleep anywhere.
That's just my opinion, anyway. There are many other theories, and nothing can be actually proved. One of the things that I found fascinating about Yume Nikki was that there was no obvious storyline and that there was no conection between the worlds; by connection I mean, you were in a snow world and you randomly find yourself in a place full of water. With baloons. Or you were at this place full of blocks, and you got into a door that led you to a monochrome world.
Kikiyama probably added things he thought of randomly and interconected them without really making sense. It's possibly the same for effects, and characters, and dream creatures.
I don't think a game this vague could have any limit for theories, and they shouldn't be discarded. After all, I don't think I ever met someone who didn't want to know why Madotsuki had strange dreams.
(But the rape theories are getting old. Some of them are good, but some are...uh)
long post is long