Yeah, good points. But you also have to remember the Showrunners are well known for playing fast and loose with what is considered canon in the comics and a lot of times to an unrecognizable degree. To name some examples:
1. Linda Park of Earth-2 is Dr. Light when that title belongs to Kimiyo Hoshi (or Arthur Light to those who are tempted to cough and point this out to me).
2. Wally is white not black and he is not Iris's brother, he is her nephew.
3. Jay Garrick exists in the same universe as Barry, but in this show he's from Earth-3.
4. Caitlin Snow is Killer Frost not a genius scientist.
5. Vibe is a lame third-rate Super-Hero who doesn't even work with the Flash not a genius scientist who actually does.
6. Dr. Wells? Completely new creation.
7. Zoom. Nothing at all like his comic counterpart. Plus, he's a Wally's villain not a Barry's villain.
I can list more examples, but that would go into minor details like hair color and such. Now, I might get flak from some people for this post but let me make myself clear on something. I am NOT complaining for the thousandth time about any of these! I am simply naming them as changes that the Showrunners have made, proving they play fast and loose with what is canon.
So. What is the ultimate point I am trying to make? It's this. Don't expect "Flashpoint" to be anything at all like it was in the comics. For one thing, no Wonder Woman war with Aquaman. For another, no Superman or Batman. There will be a lot of changes, but some form of this storyline will happen now that Barry has done one of most idiotic things in the history of his career.
Every comic show and movie always tweaks the canon and characters, somethings that work great in the comics do NOT translate well to the screen.
The first Xmen movie, Wolverine comments about the uniforms and Cyclops says "would you rather have yellow spandex?"
Spiderman with organic webshooters, which is logical, instead of mechanicals.
Most of the time the changes are good. I have no major gripes about the changes made to characters and canon on the Flash.
as to Flashpoint, I wish they wouldn't do it. But they will.