I'm skipping over posts but my "theory" on it is basically taking how things happened with Barry's story in the comics pre-Crisis and after he came back.
Prime Timeline: Barry's mother isn't murdered, still becomes the Flash through the same circumstances except he's not infused with the Speed Force immediately or have such great access to it so soon, has a generally happy trauma free life, gets involved with Iris early on and things happen as they do. No Caitlin, no Cisco, no Wells, Barry's progress is much slower. Zoom/Whatever you want to call him goes back and kills Barry's mother and you can pretty much gleam most of what happened in this timeline from the comics.
Now, either you could have...
Time Split A: Nora is murdered, Henry goes to prison, young Barry was late getting home and much of the rebooted Barry Allen story happens, everything happens as it's still destined to, Barry gets his powers again with out the particle accelerator "accident" and again no STAR Labs team. Everything happens though as it still should, including Iris and Barry getting together and so on, the Crisis happens and whatever. Eventually Barry chases Professor Zoom who perhaps has decided that more needs to be done to Barry. Barry discovers it was Professor Zoom who murdered his mom they fight around Nora but this time it happened later so Barry is , hell Flash Point could've come from this instance and we'll never see it. Things are changed again.
Time Split B: The new timeline that we're currently watching. Barry is home this time with Nora's murder happening at night things happen similarly to TSA but Future Barry shows up and fights with PZ but Barry realizing that due to Professor Zoom's previous time traveling shenanigans Barry can't save his mother and instead spares his younger self from witnessing Nora's murder. Professor Zoom decides he's going to need to do more to make Barry "better", perhaps with some help, goes back but doing so gets stuck in the past as his suit loses power. Establishes himself as Harrison Wells and uses his knowledge of the future. Wells main goal is to make TSB Barry all that he can been and sooner for his own insane interest in making the Flash the best hero he can be along with some other goal that we don't know about yet. I should probably include Eddie in TSA though that seems like something Wells could've put into motion as well, I think Wells has also learned this time from first hand observation is that Barry was always going to be a hero without the loss of those close to him and pushing himself and it could've been channeled differently or something.
Always possible that RF/PZ went back further and screwed with things even more than we already know. They've left themselves a big out for if they want to change the show up or have a need to tone Barry's powers down eventually. I do think Barry would've been the Flash regardless of his mother dying, just like they've been hammering home with the "lightning chose you Barry" thing, it was his destiny to be the Flash. Nora was a casualty of Professor Zoom wanting to ruin Barry's life.
It's late, I probably should've waited until I slept to write this and of course Time Split A could be what we're watching now. I'm kinda sorta mixing Zoom/Professor Zoom on purpose because I do think they're going to do the same for the most part. :\:\