There are many reasons why people would rather buy their own e-liquid, rather than buy prepackaged cartomizers.

Cost. Filling your own electronic cigarettes with e-liquid, will cut the cost of your vaping significantly. It depends on what and where you’ll buy, but using your own e-liquid will usually mean paying a fraction of the cost of pre-packaged cartomizers.
Choice of base. For those who are sensitive to the usual PG (proplyene glycol) base, you have the ability to buy VG (vegetable glycerine) base liquid instead. Most e-cigarette companies selling prepackaged carts don’t offer that option.
Flavors. There’s a vast array of flavor possibilities available to you when you purchase your e-juice separately; the number of flavors available from the big e-cigarette manufacturers is much smaller. There are also companies that will let you customize your smoke juice with nicotine and strength options not available in the prepackaged products.
Control over the quality of your experience. Most e-cig manufacturers don’t even tell you where their products are made, let alone how they are made. Many e-juice manufacturers (particularly the ones that are US-based) provide all of that information, and more, on their websites before you buy.
Fun. If you’re so inclined, filling your own cartridges and experimenting with various products and flavors can be a hobby, much like pipe smoking or cooking. The more you do it, the more fun it can become.