I agree with you.
Well's is using technology to make him fast. And the time he tried to use his powers and collapsed, makes me think he's jury-rigged the ability to go fast, and there's another RF that went rogue that Wells maybe had something to do with creating. Maybe his invention turned against him, and went evil and tried to kill the Flash of the past (maybe even before he was born). Wells might be here to ensure there is a Flash to fight the evil RF of the future. It still doesn't explain why Wells stabbed Stagg. Unless Stagg was has a hand in the evil involving RF.
My head is spinning already
On a separate note, i'm dying to see Flash use his powers more - like vibrating so fast those steel spikes the general set upon him passed right through him.
Or when Firestorm dropped him from the sky, spinning his two arms like propellers to slow his descent.
Running super-fast to extinguish the burning phosphorous was as close as it's gotten to this yet.