Hmmm, I'm surprised that by simply not enjoying the story as much as some of the other forum members I'm somehow less mature and should stick to Ninja Gaiden. For the record several stories in games have captivated me, Xenogears, Chrono Trigger and Final Fantasy Tactics to name a few. Xenogears, in particular, will always be the standard for me in terms of story telling in games.
But Aquaria...
Where I think Aquaria fell short was in the voice acting (Yes, I know, it was low budget, it just bothered me), the sudden addition and over simplification of the relationship with Li, the often over acted emotional scenes, and the massive gaps in game play where nothing happens spotted with huge story points that seem to throw the whole back story at you in bursts. Theres something to be said for flow. In regards to the nuts and bolts of the plot it's honestly not that hard to come up with a "deep" concept, as its been done time and time in other games. Its mostly a matter of recycling ideas in clever ways and dressing it up so that its entertaining to the player. Every once and a while a new and exciting story comes around that really catches you off guard (ie. the three games I listed above), but most are just the same old jumbled around with new faces, and thats fine! I just enjoy a little polish with those games, which Aquaria lacked.
But even though I'm being hard on the story I really did enjoy the game play. The combat was smooth, the environments were well designed, the bosses were challenging. The song system brought a sincere sense of difficulty and, at times, panic when surrounded by enemies before I realized I could use the number keys to switch effortlessly =P. My only gripe is that character upgrading came primarily through food farming (which wasn't even necessary to beat most bosses) and form acquisition, which would be nice if most of the forms weren't a simple gimmick to get through barriers. I suppose I'm still a fan of the item system used in Castle Vania Symphony of the Night, which is still my #1 side scroller. It created a nice sense of character development which I found lacking in Aquaria. You could grab new armor, but their effects were largely worthless barring one incredibly overpowered silly looking suit ;-). I'm sure one of the main reasons for this is that programming in a huge item database and balancing bosses accordingly would be much much much more time consuming and for a small dev team, thats not always an option.
So all in all, Great gameplay, average plot, sub par story telling, sub par character development. I'd still buy it again if I could go back. = )