16-18? Wow. Took me more than 25 to finish, will probably be about 35 by the time I find the few treasures I'm still missing. But then, I'm obsessive about exploring.
I can see how the time spent travelling can be off-putting. Still, I'd say that 75% of the time or better there's something interesting to be doing on the way to wherever your ultimate destination is.
The thing is, I don't think that Aquaria is the type of game you think it is, or perhaps want it to be. Aquaria is not a follow-the-story type of game, or even a goal-oriented game (to a point). Yes, there's an undercurrent of story (no pun intended), but that's not the game. If it was, I'd have hoped the story would have been a little clearer in the end.

The game itself is about exploring the amazing world of Aquaria. There's only about four instances where you have a find-the-key dynamic, unless you count having to gain a form elsewhere to get through an obstacle. And you don't really have to return to most areas once you complete them unless you just rush through it and miss something.
I've never really understood the complaint about save points. I don't think I'd like automatic saves or anything like that. An automatic save may work in more linear games (most FPS campaigns, a number of RPGs), but would certainly have hurt me if I was in trouble over my head. "Save anywhere" might work, but it might lend itself to abuse during the trickier sections, unless there's a stipulation like "must be standing still with no enemies in immediate area" or something. There was probably a reason Derek and Alec chose the method they did, and I think it's appropriate to this situation. Not all, but this one.
I don't see how one could condense the world like you describe without completely changing the game. Shrink the game down and many things would have to be cut, or the regions made more linear. Plus, I think there'd be a loss of world realism; real life has plenty of dead space (try living in a small town) and the open areas of Aquaria makes it feel much more realistic--to me, at least.
Aquaria isn't a game to push through in an effort to beat, it's a game to sit back and absorb. If that's not what you're looking for, that's fine. I don't think it's a mark against the game, though.