Deciding between "universal-fit" or "custom-fit" designs is the first order of business. It's important to note that more custom-fit choices exist, especially if you've got a SUV.
Universal Covers
A certain-sized universal-fit cover is made to fit a number of similar vehicles - not just yours. Because of economies of scale, universal covers typically sell for less than custom-fit ones made of the exact same material.
Because universal covers are made for an "average car" that's approximately the same size as yours, it won't have pockets positioned exactly where your mirrors or antenna are. Elastic ribbing along all bottom edges will help keep a universal cover snugly attached, but there's no guarantee it won't blow off the vehicle completely unless additional means are used to lash it down. It may also fit too tightly or too loosely.
A cover that's too tight may put undue stress on parts such as mirrors or spoilers, damaging them or body areas where they're attached. A too-tight cover may also be more difficult to remove and install. If used outdoors, a cover that's too loose can actually cause damage to paint and trim by flapping against the body when wind gets underneath it. If sand and dirt blow underneath a loose cover also, abrasive paint damage occurs.
Custom-Fit Covers
A custom-fit cover is specially made to match all contours of your make and model, fitting like a glove over mirrors and other items. With a custom-fit cover, accommodations for things like hood scoops, mirrors, and spoilers can be provided easily.
A custom-fit cover will usually cost more than a universal cover. But depending on how and where you plan to use your cover, any upfront savings may turn into false economy if a universal cover ends up damaging vehicle's finish. A custom-fit car cover that's well-suited to your particular use will provide the most protection.