Eh, I justified it as her being born/built/created specifically to destroy Ares. As such, her actions are less her own conscious abilities and more just a counter to everything Ares would think to do. Across media - current and ancient, alike - the big bad super-powerful being is also woefully predictable. Her lack of GODMODE in BvS and Justice League are more a function of “that’s not how she works”. Justice League dealt with the character issues, a bit. She was still incredibly powerful, fast, and strong, but there were definite hints of confidence issues and lack of leadership ability.
It’s a significant issue for most sci-fi and fantasy series, especially if they outlive the original story arc - you can’t go back to fighting minor villains after saving the world, so you need a bigger badder baddy. I think the modern Wolverine arc is probably the only one I’ve seen successfully counteract it - eventually, your hero has to die, preferably doing hero stuff. It ruins it when you magically bring the hero back in the next movie, however (looking at you, Superman).
Wonder Woman’s struggles in this movie consisted of 1) she wants to do something, 2) someone tells her she can’t do that, and 3) she does it anyway and succeeds. That is, not really struggles.
The movie showed her using that same power when sparring against the other Amazons.
Your two points are related. The reason Hippolyta didn’t want her to train was that she would eventually get pushed far enough to call up her powers, which would alert Ares to her. Minutes after the scene where she first uses her powers, the privacy shield of the island is breached and events begin leading her towards conflict with Ares.
The whole point of a Mary Sue is that you don’t need to have any special insight. It’s blindingly obvious that the author is dropping into an established universe a character that’s nothing but an idealized version of himself or herself who becomes the center of the story. If it’s not obvious, it’s not a Mary Sue.