What if Wells is Barry, and the reason he has gone missing in the future is that he has travelled back in time to the past to try to prevent himself from going missing in the future? So he's created this temporal paradox and also the future headline, and is now trying to free himself from the loop.
Agreed, and this has been my theory ever since the fourth episode:
http://forums.superherohype.com/showpost.php?p=30005443&postcount=78
(Although, my theory on the Reverse Flash's identity has changed somewhat)
And, ever since then, there's been other "clues" if you will that suggest Wells is Barry from an alternate future as well:
*Wells knowing the exact speed at which Flash needs to run on water. Does seem like something a speedster with lots of experience would know.
*His compassion towards Grodd against Elling's experiments. Being that we know Grodd becomes a super-villain as would Barry, it stands to reason that reason that treating Grodd with compassion before he develops his powers would be an attempt to prevent him becoming evil.
*His discouraging Joe Wells to stop looking into the murder of Barry's mother and being evasive about the possibility of someone else with super-speed is obviously done to prevent him from getting close to the truth, but also to protect Joe. After all, Wells appears to like Joe which, if he's really a future Barry, makes sense as Joe is essentially his second father.
*The way Wells talked about losing his wife. Now, of course, since Wells is from the future, it's clear he's not being entirely honest here. However, the way he talks about his wife's loss, the idea of starting over and getting back what he lost seems really sincere. If Wells is really Barry, I think when he was talking about his wife, he was talking about Iris. And it also goes into the motives of why he's doing what he was doing. Oh, and if there was indeed a real Dr. Wells whose wife died in a car accident, how much you want to bet that the real Dr. Wells doesn't look like the man we think is Dr. Wells?
*His wanting Barry to increase his speed? Well, obviously, if Wells is Barry and has come from the future, then he'd want present day Barry to increase his speed fast enough to break the space-time barrier, too.
*His reaction towards the changing newspaper headline--notice he didn't really start losing his cool
until Gideon told him there were no records of the Flash at all.
*Notice how when Blackout arrived as they were trying to escape, Wells' wheelchair shorted out? Then, as Cisco and Caitlin ran over to Barry as Blackout was him, Wells is suddenly behind Blackout at the far end of the garage in his wheelchair. So how did Wells get behind Blackout completely unnoticed by everyone
when his wheelchair has been shorted out? Unless he had super speed?
*Also, his directing Blackout's attention away from the others towards him is clearly meant to motivate Barry, knowing that his lack of speed is psychological, and having figured out that Barry caring for those close to him is what motivates him. Also, it seemed to me that Wells wasn't the least bit phased when moved by Barry like others have been any time Barry rescued them...perhaps because Wells is used to super-speed?
*His wanting to collect Blackout's blood to find out how he's able to make Flash lose his powers. Well, it can't be for the purposes of him wanting to try and make Barry lose his powers given how he needs Barry to go faster and his panic over the headline changing. Not to mention it would also go against how The Flash is his "greatest creation" or some such. But, if he's Barry from the future, he knows there's another speedster out there--The Reverse Flash.
Granted, perhaps I'm reading a bit too much into this, but the main thing is the show is trying way too hard to make the audience think Wells is evil, and the idea that Wells is really a future version of Barry would definitely throw the audience through a loop.