After having played Aquaria solidly for 4 days and beaten it, there are a few things that I think could use a little tweaking.
One thing that is quite different about Aquaria compared to other action/adventure type games is that the standard abilities don't get strengthened over time at all, they only get temporarily stronger after eating food. There were a couple of ideas I had around this to make the game a bit more progressive in this manner:
1. The first time Naija breaches the veil, the standard energy attack could be buffed a little - this would make it a more powerful experience. I think halfway between the strength of the regular attack and the +1 attack. This should also have graphics that are halfway between the regular and +1 attack, to make it obvious the strength has increased. +1 (and +2, +3 etc) would still be as powerful as normal, just the base attack should be buffed. Towards the end of the game the enemies require lots of attacks to kill and it gets a bit tedious.
2. The abaddon's should have their HPs dropped by 50%, they are very difficult to kill at the moment.
3. When getting nature form, the default defence for Naija should be increased by 1 point. Eating a +1 defense food would be in addition to this also (so effectively she'd have 2 defense). This defence increase would help Naija in all her forms, not just nature. At the moment nature form is definitely the weakest of her forms, and this would give people a reason to go for Nature form earlier than they otherwise might.
4. Increase drop rate for food items. I know you can re-enter a level over and over and farm items, but really it's just tedious. I see that some of the creatures have very low chances of dropping particular ingredients, like 2% chances for various things. Thinking about this logically, it means if you kill that enemy 100 times, it'll drop that ingredient only twice. This is fine if the enemy is a common one, but if there are only 3 or 4 (or 1?) of them in the game, essentially this becomes a huge pinata and most players would never see that item drop from that enemy. I think these should be increased, and also creatures that have chances to drop different items should be changed to potentially drop multiple items: eg instead of 40% plant leaf, 60% fish meat and they always drop one or the other, it should be cumulative: so 24% of the time they'd drop both, 16% of the time only plant leaf, 36% of the time only fish meat and 24% of the time nothing.
If anyone wants to take these ideas and go ahead with them, feel free. I've poked around the entity files but can't see what controls the veil event. In terms of implementation I think you could add a flag that is set, and then when Naija goes to attack, check the flag and if true generate the (new) more powerful projectile in place of the original one.
Edit: I've just looked at the Aquaria Native mod, and when you breach the Veil it doesn't do anything special there, and there aren't any special entities or nodes that I can spot. So I guess the veil-breach is something hard-coded into the game that can't be edited just through scripts and entities? I guess other mod-makers have probably run into this already. Annoying.
I thought of something else that could use tweaking:
When you go out of the water, even at a very slight velocity, you get rocketed really far up into the air, which is silly. It makes a lot of the bubble-jumping parts particularly difficult if you're actually trying to boost yourself from bubble to bubble - it's much easier to cross the frozen veil just by regular swimming, for example. It'd make sense if this were changed so your jump distance/velocity out of the water was tied much more closely with the speed with which you actually left the water - a slight boost would be ok, but not a huge one like now. And when you are going as fast as Naija can go, you should still boost as far as is possible at the moment. To put it in general maths terms, the current exit-water velocity formula feels like this: 100 + velocity. It should be something more like this: 10 + velocity * 10.
Another thing that really should be fixed, which relates directly to the above (fixing the above would go a great deal to minimizing this, however) is that when the water level drops, as in the sun temple, Naija stays where she is, but the game thinks she's left the water and therefore rockets her into the sky. This is particularly annoying coming up to the sun temple boss, where the water level drops on you suddenly and you go flying out up into the air and hit on the spikey balls and get hurt. This comes across as very unfair and strange to the player, especially when it happens over and over again - the only thing that has changed is the water level, so why are you now flying upwards into some spikey balls?