I could see them doing a very limited version of Flashpoint, (very scaled down without any of the other superheroes or villains except maybe the Rogues and Arrow) but even that would be awesome.
I mean, even if they showed an alternate timeline in which Barry saves his mom, and then of course alters the timeline (he captures RF and brings him back to the present - well, his present in 2015)
When he returns to his own time, his powers are gone, and none of the people he knew are the same (probably sad or evil versions of themselves) plus there will be other consequences (maybe Iris will be dead or he won't be able to save her). Maybe the Rogues are running the city, without Flash to stop them.
Anyway, the world is a mess - and it would be cool to see darker versions of the Arrow cast- and Barry realises after talking to a captive Thawne (no powers either, since Barry was his source) that he has to find a way to restore his powers - which forces he and Thawne to work together.
Then, they go back in time and stop Barry from saving his mother, restore the timeline and go their separate ways - vowing to continue their fight next time they meet.
Anyway, plenty of you guys have probably thought of something similar - I think it would make a great 2 or 3 part story.
So, in answer to the OP, yes a Flashpoint story would definitely work (now that the time-travel door has been opened), however, I think it would be a very downscale version - they have to work with what they've got.
Still, any version would be awesome if the writers take the same care they've taken with the whole RF plot so far !