I agree about some of the annoyances of the original Yume Nikki. Let's not glorify it as a game. Lots of empty, giant rooms and slow waking speed make for a pretty bad game experience until you accidentally find the bike or use a walkthrough. (And there is another big then that remains unclear in a blind playthrough: how to go about solving the puzzles, if there are any. I wish Kikiyama would've put something in the "instructions" effect that would tell you there are basically none in the game.)
I also agree with the other point - there's not really enough areas in the game to constitute it being like a real dream. You would almost think its more like Madotsuki going into a fantasy world in day-dream fashion than actually falling asleep. Besides the random chances around particular hidden events in the game, there isn't much randomness either, like the kind you see in LSD: Dream Emulator. (Although that game gets limited in that by other ways.)
Initially, Yume Nikki came off as a boring and level-design wise, poorly designed. It was only after seeing a lot of the areas and events, and knowing the ending wasn't out of place that I begun to appreciate the game. In a way, you don't know how pretentious a game like YN is until you know the ending. Luckily, it avoids coming off as pretentious and seems deep and meaningful instead. The game was a metaphorical hell-prison, and it would seem the message is to "never return." And of course, in regular game and sequel style, you return in the fan-games, lessening that deep point.
I think the fan games need to go far outside the bounds of the original to become valuable in the same way, and I don't know how it would be done, but maybe someone with a creative enough mind does.