Recent episodes imply that Eobard Thawne designed the particle acellerator to malfunction and give Barry his speed but isn't that leaving a lot to chance? Assuming it even affected Barry how could Thawne be certain it wouldn't cause Barry to develop different abilities - or vapourize him altogether?
Thawne didn't have to do anything special. Barry's special, he's not a normal meta-human; the Speed Force chose him, and imbued him with stupendous power. Thawne merely needed to mimic the conditions that originally created the Flash, and it would have the same result. Barry's destined to become the Flash, Thawne merely sped up the timeline.
We see this (in addition to dialogue outright stating it) in Barry not just getting his powers from the particle accelerator, but also being struck by lightning. When his powers were drained, another shock of electricity not only returned his powers, it unlocked the full potential of his power, which has since allowed him to travel fast enough to pierce the time barrier.