In the 1st season of The Flash we see that Thawne is faster than Flash. Then why did he need Barry to time travel to his to open the portal, why didn't he run fast?
Though Thawne could run faster than Barry, he never had the full grasp on speed-force. Eventually, he lost the connection with speed-force just after killing Nora. That's why he had to re-create the particle accelerator explosion to give Barry the speed so that he might help him go back to his time. However, he could charge up himself with tachyon pulse generator; but that's another point.
But the crux is that Thawne could time-travel but for some reasons he lost his connection with speed-force.
The comics give a better explanation during the Flashpoint crossover event (which is what season 1 of Flash was VERY loosely based on).
At the point where Thawne had killed Nora, Barry's life changed enough that he wouldn't become the Flash. The comics show that Barry doesn't just tap into the Speed Force, he actually generates it across time and space with every step that he runs. This hasn't been explained in the show yet. Thawne couldn't access it because it never existed, hence his need to become Wells, cause the particle accelerator explosion much sooner than originally it would happen, and train Barry up for max speed, to generate a speed force that was accessible even in the future where he was from.
Strongly recommend the Flashpoint crossover; you'll find a lot of background information that explains quite a lot (if you squint at it sideways a little anyway)