I think when Thawne used that genetic camouflage it not only changed his outer appearance, but it also "bled" Wells' knowledge and memories into Thawne.
I think this is the reason Wells has a good side to him.
Every time Barry says "I can't" when trying something impossible, Wells always delivers a motivating speech/message which pushes Barry to the next level. I think if the real Thawne was in full control of the personality, he wouldn't be such a sweetheart with Barry, Cisco, etc. the only time we see Thawne "come out" is as RF and when he's off making someone "disappear". I'm of course using the reveal of the real RF as a reference to his actual personality.
Thawne may be smart, but he's not Harrison Wells smart. Just because he stole his face, doesn't make him make instantly know how to create the shit that caused the accident and Barry to get his powers. It just wouldn't make sense if he only stole his face, he even said "I need you to make that device (I forget the fucking name) a little earlier than 2020".. Killing him wouldn't make that happen, but stealing Wells' knowledge and memories is what would make him capable of building the machine. Just because you know what happens in the past, even with the information, doesn't mean you'd be able to make it.
Wells is in there, somewhere.
Oh and btw, Flash's streak is read, not yellow.. Which is why Iris dubbed him the red streak in earlier episodes. In close ups you can see some yellow lightning but when zoomed out it looks like a glowing red. RF has yellow streaks when running. I know it's supposed to be the other way around (comics and animation) but it appears red.
http://ia.media-imdb.com/images/M/MV5BMTQ5MzY5ODE5M15BMl5BanBnXkFtZTgwNzU4OTM1MjE@._V1_.jpg In case pic won't show