pika pal:
Those are almost all my exact points! I linked to the post where I gave my opinion on Zinnia, though I'll comment on the points you did that I didn't:
All Those Keystone: Yeah, why did Zinnia senselessly steal the Key Stones, one which lead to our neighbor rival being beaten up (which I don't think Zinnia EVER apologizes for. Yeah she gave the Key Stone back but that's after the events, during the story I wanted to kick her butt. And let's not forget that on Sky Pillar she knocks your out for no reason, like we weren't going to wait or the thing that'll save the world which she forced us into doing? And yet she's surprised she's unworthy to Mega Evolve Rayquaza). I guess she was having problem getting Rayquaza to appear to thought gathering a lot of Key Stones in one spot would attract it which I guess it did... but still it would have done nothing if the player wasn't there.
Thinking about it Rayquaza is also a bit of a jerk, it lost the power to Mega Evolve so instead of maybe summoning/appearing to someone to help it reclaim its power it instead doesn't appear (which led Zinnia on her Key Stone hunt). And why did it decide to appear after Zinnia got all the Key Stones? Did it too think maybe the energy from all the Key Stones would make it Mega Evolve?
Wally thankfully ignored a beating by leaving his Key Stone in his room when he's staying at home so Zinnia stole it when he was out of his room. But she probably would have pushed him down to take his Key Stone had he had it on him, meaning she would be perfectly fine beating up a kid with a health condition. Our "protagonist", ladies and gentlemen!
Could Have Told Someone: As you pointed out, at ANY time she could have gone to Wallace. That's all she needed to do so that everyone start following her plan. Now admittedly the science community might not have believed a meteor was heading toward them since I think they would have detected a 4 mile meteor heading toward the planet WAY before it was at risk of hitting the planet so this had to be a sudden thing (and since it had Deoxys in it I woudln't be surprised if by some capacity it was controlling the meteor's movements). But still Wally, who knew about the myth, would have believed her and maybe at least started some initial planning since he's, you know, a Gym Leader so had some sway (as well as being best friends with Steven, the Champion). She then wouldn't have need to tell Team Aqua/Magma about the Orb and almost cause the end of the world AND the scientists would have saved the Link Cable as a Plan B.
Because You're The Player: Yeah, its very odd Zinnia is super friendly with you upon first meeting you. I guess she maybe gained respect for you after you stopped the Legendaries, but considering her plan wouldn't she be mad you stopped her (unless she realized her plan wasn't working)? Like maybe I could see her being kind to you after defeating her in a Pokemon Battle, proving you're stronger than her so she decided to befriend you (which would be just another way she's trying to manipulate things), but when you first meet her technically she's on the run for just stealing your neighbor rival's Key Stone (and beating them up) and yet she just strolls up to you and talks for a bit. You egotistical B****! Anyway, her being kind to you is just because you're the player, no other reason explain it. She shows no respect for ANYONE else, not even the (former) Champion who honestly has more sway then the player does. I can only think maybe she knows you can't defeat you, something she confirmed in Granite Cave, so decides to manipulate you by acting as a friend. If you lost she'd probably would have also stole your Key Stone, but she couldn't so she had to come up with another plan to get you where she wants you to go.
And then we're suppose to feel bad for her because she lost someone close to her. Look, I'll feel bad for Aster since whoever she was she did do something that cost her life, but I won't feel bad for Zinnia since she went WAY out of line to get what she wanted done and caused pain in others doing so.
Another one of my favorites: Emboar is said to light its fist on fire when fighting. Emboar cannot learn Fire Punch unless from a Move Tutor... what?