[Spoiler Alert!] If you have yet to see the phenomenal mid-season finale of The Flash, then I'd advise you don't read this article. Unless you're one of those people (like myself) who likes inquiring into spoilers and works out what's happening and what's going to happen based on educated conclusions from comic book sources. But that being said, this is a pretty big one....
With that aside, lets get down to what we all want to hear... The Man In The Yellow Suit was an amazing episode and, from what we are given as obvious facts, we can only assume that Dr Harrison Wells is 'The Man In The Yellow Suit'. Of course all the information provided by the show has pointed to this theory, has it not? We've been shown he possesses what could be The Silver Age Suit as well as The Tachyon Device.
So from the evidence provided, Wells seems to be the likely suspect for being The Man In The Yellow Suit. Personally, I think not.
Actually, what the show has shown us thus far is that we have many reasons to believe that Wells is anything but Barry's enemy. He has been there from the beginning supporting Barry so he can help cure all these diseases but once again I don't believe thats the case. What he really needs Barry's commitment and speed for is training and preparation for the future.
My personal theory, that I assume to be correct, is that obviously Wells is part of Barry's future team and this is one of the reasons he is in the past acting as a guardian of sorts towards Barry.
But he's only back here because he came to stop an older Barry from stopping Professor Zoom (Eddie) from killing his mother, which would result in him never becoming the Flash. Whilst Zoom and Barry got trapped in a time rift, Wells was stuck in that time period. This is why Wells often looks at the news article where The Flash is missing. These events are suspected to have caused this.
Wells knows that all this has to happen, so creates a version of The Silver Age suit, a Flash suit that allows Barry to have his powers without actually having them. In the comics it is naturally Red until Zoom finds it in a time capsule and alters it using a machine which reverses the flash emblem and changes the color scheme. In the show it seems that all this has already been done so maybe Wells has take this from Zoom and uses it to his advantage?
That advantage being, that Wells needs to teach Barry that he has to be able to match and beat the suits speed so that when Eddie/Zoom eventually does take possession of this then he will be able to beat him. Wells also sparks conflict between the them before they've actually met by creating this early bond between the two so he can train without realizing it.
This leaves him ready for when Eddie steals the suit in the future and he'll be able to beat him, but in the meantime Wells is to help Barry with his abilities and hope that he can prevent him from being trapped in the time paradox in the future. Barry is being trained to fight Zoom with the Tachyon Device which enhances Zooms speed so when he doesn't actually have possession of it beating him will be that little bit easier.
Good Theory!! Or Is It??
The one questionable thing here is that if Wells is trying to help better the future and stop this crisis then why hasn't he just stopped all of Barry's enemies before they become major Justice League problems??
There is a simple answer to that and it is that your enemies are the ones who define you. Wells created the Silver-age Suit knowing one day Eddie would claim possession of it. Just as he could've stopped Cisco from creating Captain Colds cryo gun. He has been providing Barry with the training and skills necessary to take on enemies such as Captain Cold, Professor Zoom and Gorilla Grodd in the future. It's what his enemies do that cause him to perform/execute a counter measure which is what makes/changes history.
Without these enemies the future would have been changed. We've already seen that the slightest things change the future that he intends to preserve and protect so he couldn't not create these enemies for Barry to face. These need to exist for things to happen throughout the DC universe. He needs these enemies to be created so that Barry can become The Flash that the world needs without altering the future.