Hey, I also completed this mod now, and wanted to leave some comments.
First of all, thanks for creating it... I really enjoyed it!
As for the above discussion about the intro map enemies being too difficult, I disagree. I found it quite easy to simply swim and jump around in such a way that they could not hit me. (And I don't even consider myself a good player...) Yes, swordfish can be annoying, but you can easily see when they're going to jump at you (they stand still for a second or so right before), so that's when you know that you need to dodge. Sharks aren't all that difficult, as long as you don't stay in the same horizontal line as them. And the giant wurms can be intimidating, but since you're faster than them I don't see the problem. (Also, once you find the bind song, you can fight them by dropping stones on their heads...

)
Aristobulus, is it possible that due to the original game you had become so accustomed to energy form that you had forgotten how to survive by simply dodging stuff?

Also, if you're having trouble
here, wait until you reach the "Depths" map (see below)...

I do agree that the anemones can pose a challenge though. The first time I jumped off that cliff into the unknown, I landed right on the anemones, and got bounced off of them (without being able to do anything about it) ... right into some more anemones. Outch.
Anyways, the feedback I wanted to give about this mod:
1) What I especially liked- Naijas's home. It's small and cozy, and actually feels like a home. In the original game, I was always annoyed by how big the home cave was - especially with all the extra rooms (or should I say halls) that got unlocked as you advanced in the game - and the treasures got spread out over all this vast space, which denied the player the satisfaction of seeing an overview of all found treasures close together. Not so in this mod.
- The "Rapids" map. I thought this was a really innovative and fun puzzle. And thanks to the strong currents and wormholes, each "try" through it was relatively quick, so it didn't become obnoxious to do many tries.
(Although I am wondering whether I missed anything useful, since one time I ended up in a dead-end that had a song plant, so maybe there were more songplants or costumes there that I missed?)
- The "Strange" map. This was simply awesome. Beautiful graphics, lots of fun jumping opportunities, an abundance of strange "fish" (they dropped fish meat and oil, so I think I can call them that...
), and an interesting boss fight (where it's not immediately clear how you can even have a chance to defeat him, but once you figure it out it's quite doable). Also, this map really put the fun in wearing the Urchin costume (which I never found much use for in the original game)...
- The zoom spots in the main "Wheel" map. Great idea, and well executed.
- The background graphics in the "Pearlmine" map. Various places in this map gave a really cool "depth" feeling, like you're actually in a big 3D world. No place in the original game achieved that so well.
2) What I found (positively) surprising- Ok, this is not so much about the game itself but rather about my experience with it. When I first started exploring the central "Wheel" map, I thought I would never be able to find my way around it, and it would be one long, tiring journey of trial and error 'til the end. But by the end of the mod, I suddenly realized I had come to "know" that area quite naturally and could quite accurately find my way to specific points of interest without even putting much thought into it. A rather nice learning experience...
3) What I found a little irritating- The rukh nest in the intro map - because it did not leave a "rukh egg" ingredient like the two rukh nests in the main game do...

- The section in the main "Wheel" map that was filled with Nudibranchs. Ok, maybe I'm simply angry at myself because for some reason it took me quite some time (and several deaths) to solve that "puzzle". But even once I had figured out how to do it, it was a tedious task to actually execute (a long way of swimming back to various earlier points, and returning) . Couldn't that puzzle have been more locally confined? I.e. only a short tunnel section filled with Nudibranchs, with both sides of it easily reachable without having to swim for 10 Minutes (accounting for getting lost along the way)?
- The Octopus boss fight. In most boss fights in Aquaria you 1. need to figure out how you can damage him, 2. plan how exactly your'e going move and what steps you're going to take (e.g. jump back and forth between specific spots, swim around him in a specific direction, damage him at very specific times etc.), and 3. execute it three or so times until he gets mad, then 4. blast his eyes. If you didn't follow your well-planned steps for how to move/act, you would usually get killed fast. If you did, you would win.
In this mod's octopus fight, on the other hand, I couldn't figure out any such steps - the octopus simply moved around and used his weapons too erratically. On the other hand, he seemed to have much fewer hit points and would do less damage with his lasers then the Aquaria-bosses. So it degenerated into just a messy close-range hustle between me, my bound rock, and the octopus - with me simply accepting his laser damage and offsetting it with health recipes. When he died, it just wasn't the same feeling of satisfaction as after a carefully planned and successfully executed Aquaria boss kill.
4) What I found a little irritating, but in a way also kind of fun 
- The "Depths" map.
The sheer number of nasty enemies in this map was just... crazy :-) I found it completely impossible to do any systematic exploration of the map - I became so preoccupied with dodging missiles and running from predators that I pretty much lost my sense of space and just jumped across caves, tunnels and wormholes aimlessly (often ending up in the same spot repeatedly)... When I came across an energy shot door and associated "ball", I was actually beginning to think I had made a mistake and should have found energy form before entering this map... It took quite few more minutes of frantic swimming around before I reached a savepoint, and yet more before I at last found the "magic wormhole chamber" that would allow me to solve the map...
(Btw, once I had energy form, I systematically cleaned out the whole map, leaving no monster alive, just out of revenge...
(ok, also for the song plants))
5) What I found a little cheesy- The "recipe refill" room at the bottom of the "Wheel" map.
You could just go back and forth between that room and the jelly fish room right outside it, and they would both restock everytime so you could easily get as many leafs, eggs, red bulbs, jelly oil, etc. as you want. The kitchen was also near, making it possible to make full use of those ingredients... Of course I couldn't resist (I even took a trip back to the "Strange" map, to stock up on meat and oil (and recipes based on them), just so I could make use of all those leaves and eggs...) but in retrospect it made the game a little cheesy.
- The last boss fight (after getting energy shot).
Maybe I am myself to blame (for having stacked up so many recipes), but this wasn't so much a fight, as it was me eating some Energy shot +2, Speed +2 and Regeneration +1 items, and then jumping around and continually hitting the [CTRL] button like crazy without much tactical consideration. After some time I got blinded (screen turned into rainbow spiral) - I don't even know what caused it, I guess I was hit by some projectile - and when the screen turned normal again, I noticed all enemies had already died in the meantime and I could stop hitting [CTRL]... 
Again, all things considered I really enjoyed playing this mod, so thanks again for creating it!