I completely agree with the suggestions thus far. I'm guessing the devs didn't want to put too many save points to avoid having them be abused as recharge stations. I know having a save point do both things (save and recharge) is convenient in terms of design (since you can never save in a hopeless situation), but if the end result is that you place too few of them it kind of defeats the point.
However, the map is a big deal. Whether issues stem from engine limitations or whether it was a conscious design decision I don't know, but being limited to seeing only the room you're in really dampens the enjoyment level. Your suggestions, Lim, are all sound, though I really don't think the leaf marks are necessary. They are optional, after all, and you're just as likely to stumble onto them while navigating new areas as retreading old ones. User added notes or marks on the map would also be a sound addition, but probably not necessary. I just think a lot of frustration would be resolved if you could just navigate the different rooms in the map and see where you've been and where you haven't. This
SPOILERS follow, just in case.
I too missed Li the first time around, and for exactly the same reason, Terry. That's also a big mishap given how important he was to the game. Considering how chatty Naija was, she sure chooses odd times to keep quiet. It's something that could be fixed quite simply merely by having Naija mention how intrigued she is by him and how pressing it is that you catch up with him. I also think several boss battles could stand to be improved since they can be unnecessarily confusing the way they are now. The final Cathedral boss for example (the one you obtain beast form from): I think I spent an hour on him just avoiding his shots and shooting him in the face simply because the game was giving me (inaccurate) visual feedback that he was receiving damage when in fact he wasn't. Even after I became so frustrated that I decided to clown around and see what happened it took me perhaps thirty additional minutes to figure out I could bind the bloated frog things. The game had simply not trained me for the situation, turning what should have been an entertaining boss battle (because really, it was a pretty clever solution) into tedium.
I'd love to hear the Derek or Alec's take on some of this, particularly since the game has yet to reach its full audience. I'm guessing some of these issues stem from the limited focus testing an indie game can receive. Perhaps us early adopters can serve as expanded focus testers for the X360 and Wii versions?

While a worthwhile and memorable experience nonetheless, I think Aquaria could be raised a few notches with just a few tweaks here and there. Is the game final as it is, or might we see improvements to the experience beyond bug fixes just yet?