It's pro wrestling; it's not real. Comparisons to the NFL, UFC, or any actual sport are meaningless. The rules and logic that apply to pro wrestling championships are fictitious, just like the rules that dictate what happens in a comic book or a film. The logic of the world can be violated, and it can ruin the product. But it doesn't need to be real world logic. If it were, the Intercontinental title would be the first to go, as it has no identifiable purpose in a real sporting competition. In the world of the WWE, having two championships makes sense because the two WWE brands are supposed to be competing with each other; they have tried to steal each others talent, their general managers have often been at odds and in competition with each other, etc.
In terms of the real world value of having two titles , it offers variety. One world title would likely just pass between Cena, HHH, Orton, the Undertaker, etc. It would be dull; hell, it WAS dull. Having two champions also allows both brands to create equally important plots internal to their own rosters. And if you're also suggesting that the brand extension should end, I disagree. As with the titles, having two brands just offers variety. It allows the WWE to showcase and push more talent, and theoretically it should allow for a lighter travel schedule for the WWE's performers. It also cuts back on the over-saturation of certain wrestlers without preventing the WWE from making money from more programming. Sure, the split hasn't always been used as effectively as it could be, and the lines between brands aren't always clear, but overall the split is a good thing. At the very least, if you don't like something stupid that's being implemented on one show (say, a celebrity guest host or something), or if you don't like the roster or the title picture on one show, you can just watch the other brand. At best, the split allows the WWE to satisfy different groups of fans, such as by using Smackdown as the 'wrestling' show and RAW as the 'entertainment' show, as it's done in the past. Or by gearing one show more to an adult audience, and the other more to the PG fans.