The biggest disadvantage of using Pantry is the same as its biggest advantage: its command-line interface. Graphical user interface programs attempt to be self-documenting: just sit down, click on some buttons, and hopefully you can figure things out. With Pantry, on the other hand, you will absolutely have to read this manual to figure out how it works, and you will need some practice before you are comfortable with Pantry. In this way, Pantry resembles other command-line oriented Unix programs. As with other Unix programs, once you learn Pantry, you will love its speed and efficiency--but you will have to spend some time learning.
Similarly, because of its command-line interface, you will find that you are most efficient with Pantry if you know your way around a Unix shell prompt. For example, you will find that you can use Pantry more quickly if you know how to use your shell's features to manipulate your command history. Such knowledge is useful for any Unix command-line program, not just Pantry; however, building up this knowledge takes some time.
Pantry has no tools to graphically visualize your food intake. I might eventually add such features using Gnuplot or something similar.
A final disadvantage of using Pantry is that it is still new. I am still tweaking it, making changes, adding features, and improving the documentation. But perhaps this is not such a disadvantage: software that improves is nice. If you have any features that you would like, ask!