The answer in short is that although the less expensive scroll is perfectly kosher. That is, it conforms to the requirements of Jewish Law (Halacha), it may not be written in a very nice looking script.
This of course leads to the next question. If it's Kosher and it's rolled up and hidden away inside the cover, why do I care how nice the script is? I am never going to see it anyway. The answer is that when we do a Mitzvah, we are supposed to endeavor to do it in the nicest way possible. An example of this is that in the times of the Temple, when the people would bring their first fruits to the Holy Temple, they used to place them in beautiful baskets and decorate them with ribbons. This was in order to beautify the Mitzvah. The same applies to a Mezuzah. If one has the means to purchase a Mezuzah written in a very beautiful way, it is a good thing to do.
On the other hand, if a person has limited means it is much more important to have a basic Kosher Mezuzah on every door in your home than to put an expensive one on only a few doors. I often recommend to people to get a superior quality Mezuzah at least for their front door, in order to fulfill the idea of beautifying Mitzvahs.
Of course the other main difference would be the custom. Sephardic and Ashkenazi Jews have developed slightly different styles of script for writing the Mezuzah. Although the text is identical, the actual script of ‘font’ varies somewhat. It is important to note that a Sephardic Mezuzah is perfectly kosher for Ashkenazi Jews and vise versa. But it is preferable to use a Mezuzah written according to your family’s custom.