To expand on Juice's answer, the batteries you can get for the mods are available at multiple places but they're not proprietary batteries. Even though you can use an adapter, an eGo battery with a KR808 cart on it doesn't look like an eGo anymore, so to retain the look of some of the kit ecigs, you have to get their batteries, at a price of $18-25 with right now a maximum of 1300 mAh. The battery for one of the 'big batt' mods, an 18650, runs from 2400-3000 mAh and costs around $7-12, depending on where you get it. In addition, most are made to do high voltage vaping with a simple swap out of batteries, something that none of the Riva/eGo type are capable of at this time. And with the big battery life, even continual use of LR atties/cartos is not going to impact daily use- no need to carry around 3-4 extra batteries.
They're also sturdier. Read some of the stories about what people have done with their Silver Bullets, Chucks, and Buzz.
And maybe most importantly, the manufacturer of most mods really stand behind their product. They seem to take it personally if something goes wrong with their Reo or GG. And you'll also see the mod manufacturer's at the forefront of innovation. You don't see any 'kit' juice feeders or variable voltage, but the Ali'i does that.
There's a lot to like in mods, from a cost, function, and aesthetic viewpoint. It may take a closer look to appreciate the artisan qualities of some of them, but most are works of art in their own way.