Well, in my personal opinion, Orton isn't the best suited to win the title strictly with wrestling capabilities, but you have to look at the situation they're in. The WWE needs balance to maintain its draw at all times. If they have everyone turn heel, it goes to shit (ie NWO) and if they have everyone as a face, they have no tension. With the suspensions, injuries, and firings, they DO have the talent to produce a great show, but having 3 separate rosters kills it. Sure, someone like Kevin Thorn wouldn't be as high on a roster as he is on ECW, but is he really THAT talented? I think Thorn would be a midcard level guy on Smackdown or Raw. The more people on the 3 levels (WWE/WHC, US/IC, Miscellaneous) the more storylines you can have and the more tension. Right now, ECW has a low roster so they can't afford to lose any big guys (Punk or Morrison), Smackdown is lacking in the top card and can't afford to lose Taker or Edge who will revitalize it, and Raw only has HHH, Kennedy, Orton, Umaga, and to a certain extent, Carlito and Hardy. As a general rule, you don't give the WWE title to someone that isn't a top level guy or isn't being pushed towards that, so everyone who thinks it should be someone like Shelton Benjamin or Kane just has their hopes up for no reason...it won't happen. So that leaves us with the Raw guys. Carlito isn't deserving yet as he's between the top and midcard level and isn't receiving a push, Umaga could literally feud with ONLY HHH on the roster and that would be boring for a while (plus they just had Khali as WHC and having two guys that don't speak English on screen would be repetitive and boring). That leaves us with four: Hardy, Kennedy, Orton, HHH. Hardy, albeit a great performer, is the IC champ right now and they assuredly don't trust him enough to double-belt him and make him their #1 in the company after that 30 day suspension. Right now he's in a transitional period. They gave him the IC title because he was their best option and now he's been given the opportunity to prove his value to them, and so far he's done a nice job but they aren't about to catapult him to the top. Triple H is their #1 face, a big draw, and someone who doesn't NEED a push to be eligible for main event status. Since they have no other faces, he'll be the one "gunning for the belt". We're down to Kennedy and Orton. Kennedy is fresh off a suspension, and although he's been in line for various pushes that have all crumbled for various reasons, they won't bank on him just yet - they'll wait to push him around the Royal Rumble and build him up in the process. That leaves Orton - the guy they've been building as the top heel, considering giving the title to time and time again, and being a heel can create some much needed change in the WWE right now. Cena created a year long story of "the face is challenged by an unbeatable foe and superhumanly comes out on top" which is boring to fans after a while. Back in the days of HBK's first reign, they knew when to switch gears and have Sid win it - when the story stared to lose steam. Cena's lost steam months before his injury, so yeah, everyone has patiently waited any change and now they're getting it. With a heel as the top guy, the story now shifts focus from "everyone" rooting for the guy at the top of the hill to continue kicking down everyone who tries to climb, to now "everyone" rooting for the man on the top of the hill to be thrown off.
In one way, it'll be the same thing that we've had recently with Cena, but in opposite terms. Everyone wanted Cena to lose the championship but he'd retain by the skin of his teeth, like a heel would. Now everyone will want Orton to lose the championship but he'll cheat his way into retaining by the skin of his teeth, like a heel would. The only difference is that with a heel champion, you know for a fact that it isn't going to be long-term, so its more exciting than sitting through another face domination. When Cena was the champ, you could tell that he was going to retain because they weren't building the heels up enough to be someone that was legitimately dangerous enough to defeat him, just dangerous enough to get in a cheap shot at the end of Raw every night and lay him out so the camera can zoom up to his face grunting. The only times I've ever actually thought Cena would lose was at Wrestlemania against HBK (another guy so talented and over that he's permanently ingrained at main event status and could win the title at any moment) and when Cena was going to be in the Last Man Standing match since they were finally showing him as the one that had the upper hand.
So yeah, even though I'd much rather see HBK, Undertaker, or Edge as the #1 guy in the WWE, one of them is injured and two are on another show that needs them for stability purposes, so it won't happen. Jericho won't return at No Mercy to win the title, either. With what we have left, it makes perfect sense to give Orton the title, but if we had the full roster, it'd be a completely different story, as his backstage habits would prevent him from being their top man.