One slight difference in powers was that Barry was able to vibrate his molecules and pass through solid objects. Wally could vibrate his molecules, but would make things explode if he passed through them. Also, Wally was able to lend and borrow speed from objects, which Barry never did.
Additional Info:
Wally could make things explode, but after learning about the speed force, he was able to control this and vibrate through things without needing to. Additionally, Wally's ability to manipulate the speed force allowed him to do a lot of things Barry couldn't, most notably:
- He could run through time without the need for the cosmic treadmill (Flash #0 from Zero Hour).
And
- He could give/take speed from others (numerous).