Although 999 a good game and worth playing, I think you are being too kind on the "fast forward" feature for subsequent playthroughs. Every new bit of dialog forces you to slow down (despite most being minor changes that don't affect anything) and you still need to solve every puzzle again for each playthough. Add in the facts that there is no logical way to know which ending you are pushing towards, where endings repeat, or what order you need to get endings to receive the "real" ending and the game has some significant drawbacks.
Luckily the story is interesting and absurd enough to make it worth overlooking the issues. I'd recommend that, after getting at least one ending on your own. new players look at a FAQ or guide showing which paths to take to get different endings - and that comes from someone who is usually firmly against using FAQs while playing, especially for games like this.
Well, I disagree with you on the puzzles, because even though you do have to solve them again, the answers are the same, so all you really have to do is remember what the solution was or even write it down.
But you are completely right about the ending structure. I too resorted to a FAQ after I got the same ending 2 times. Thankfully, a kind soul on Gamefaqs has written an excellent spoiler free walkthrough. But I think the thing that really needs to be fixed in visual novels, and would really make them perfect, would be to make it clear, in some tangible, logical way, when a certain choice would affect the outcome, and why. In 999, it's not just the door choices that affect which ending you get, but it's also certain other choices and dialog options which, in retrospect after you get the true ending, make perfect sense. But only after you get the true ending-- before that, you think "Why the hell would me giving this character a certain item make the difference between a good ending and a bad ending?"
But the story is actually really good, not necessarily absurd (hell, it's less absurd than a guy who dies and becomes a smoke monster and must never, ever be let off the island because the island is like a bottle. Uh huh). And the really big twist (as opposed to the little twists along the way) is pretty mindblowing. When it happened, I actually looked around me, thinking "oh crap. Is this real?"