1. RF has been operating under a power constraint since he was stuck in the past.
2. Once the accelerator detonated and Barry got zapped the speed force was born
3. RF still needs things like the tachyon device to energize his suit with tachyons for power
4. We now also know that he had a battery in his wheelchair that pumped him full of energy.
Both that and the suit likely are what keep him faster then Barry, plus Barry's own self doubts.
But the logic error I find is this: while it is true that people want heroes and especially villains to look cool and menacing, etc etc, the fact that when in costume and in battle, RF constantly vibrates to blur his appearance and the glowing eyes.....wouldn't that be a waste of energy? Before Team Flash figured it out, yes the blurring of image and vibrating of vocal cords was a disguise so they wouldn't figure out RF was Wells/Thawne, but now that he has been outed doesn't that seem like a waste of the precious energy that RF needs to get home and then fully reenergize himself once he is back home?
Also there are some logic errors about the whole time warp to the past to kill young Barry since that would terminate the Flash existence and then RF has to make the accelerator happen a few years sooner so that he can get home thus altering the timeline already. However those logic errors can be basically put aside when one remembers that RF is a sociopathic killer who is completely obsessed/fixated on destroying Barry Allen. Afterall if RF kills Kid Barry then there is no Flash and hence no Reverse Flash, thus RF is attempting to kill Barry to the point of committing temporal suicide.
Also, if Barry really wants to start being able to trump RF in battle, one he needs to free his mind of doubts, just like Neo in the Matrix. But ALSO, Barry should either use the internet or else a library and get any and all books that teach combat skills, particularly the martial arts. Since Barry can go through books lightning fast and remember everything in it, he should be able to memorize all the combat moves in the books and then put them to some practice at hyperspeed.
Imagine if say Barry studied any and all books on Jeet Kun Do, the style created by Bruce Lee? How about Thai Kick Boxing or Tae Kwon do? Karate? Judo? Ninjitsu? Akido? If Barry were to do all that plus any books or manuals about military combat training, I bet he could easily defeat RF in battle.
I was thinking the same thing about the voice vibration in this week's episode. Why was he bothering to disguise since they know it's him?
Of course the answer may be that when he powers up as the RF, maybe he is physically changed from his Harrison Wells disguise. Or, he could have been doing it for so long that it's an automatic reflex by now, it would actually take more conscious thought and effort to NOT do it.
I figured that when he went back in time, he didn't realize that killing Barry or in effect undoing his origin, he'd lose his powers and be unable to return home (or why he'd assume he had a home to return to, might now be a future all ruled by Grodd's descendents). Maybe they'll explain it in the next issue, but if they do succeed in undoing RF's time trip, then how does Barry and the others still get their powers since there won't be an accelerator accident? I think they tied way too much to the accident and Wells/Thawne's machinations in this alternate timeline to properly address and we know that many of the characters will still be running around afterwards.