So I used the activity monitor while playing the game in windowed mode. Ever since I started having issues with game performance I will usually play with Aquaria being the only thing open. Looking at the activity monitor, the only other thing listed that used up a significant amount of RAM was something called kernel_task, which I assumed was some sort of essential system program from what I saw of it.
Keep in mind that my technical knowledge of computers is relatively limited, so I am just going to explain things as I see them and hope someone can tell me something useful

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As I was playing the monitor listed Aquarius as using up around 200mb at first and the CPU% looked reasonable, and then started to slowly increase. One thing I noticed is there was never any large amount of "free" RAM listed on the pie chart (usually around 10-15), but that as the usage increased, the section labeled "inactive" would decrease to compensate. After 10-20 minutes, when the usage of the game had hit just under 400mb and the inactive was somewhere around 200mb, the gameplay started to get choppy. The CPU usage, which had been pretty steady at a reasonable level (i think it might have been 60% or something) started yo-yoing up and down from 99% all the way down to 15%.
The only thing I can assume is the rest of the RAM left "inactive" had to be kept there for system software or something and Aquaria started needing more RAM and there wasn't any more available. My question is, is there anything I can do to smooth out my gameplay short of putting more RAM in the computer? Is the anti-aliasing thing something that would be possible at all to turn off? It seems a bit ridiculous that when the requirements listed for the game say 256mb that I wouldn't be able to run it decently on a computer with 1gb in it. At this point I am at the final boss with just about everything else in the game finished, but the performance issues have been preventing me from being able to play through the whole sequence.
Thanks for all the help so far!