It's in the house with the door where the guy says he's never been able to open it. You need 2 keys to unlock it. One of them is in a cave near the top of Silver Rise that's inaccessible during your first visit with Tristan (it's near the staircase that goes to/from the peak) and the other is in Shade Forest. In Shade Forest, there's an ice pyramid with a staircase being blocked by some boulders. You need to go around activating crystals (same as in Silver Rise) until everything in the way has been removed and you can go down the staircase. There's also a catchable level 45 Froslass down there.
I haven't played 3.1 so I don't know if her team changed along with the new ship scene, but in the original release of episode 3 she had Crobat, Cacturne, Milotic, Blaziken, Zangoose, and another Pokemon that I don't remember but it wasn't Nidoking.
If you gave Cera the Magma Stone, you need to go to the other entrance to Valor Mountain which is in Crawli's gym (past the door he enters through when he battles you on the bottom floor).
I didn't know the hooded guy who battled Heather was Corey, since I didn't find all 5 police officers (I missed the remains of the one in the library by not knowing you could walk on the bookcases). I thought he was an admin.
I remember someone asking once if there were going to be Gym Leader rematches (I think it was in the "We make Pokemon Reborn. Ask us anything" thread) and Ame said it wouldn't be much of a postgame if you couldn't.
*finds a video/post/article/etc. that looks interesting but is long*
"This looks cool, but I don't really feel like reading/watching all of it right now. I'll come back to it later."
*forgets about it for several weeks/months, and now I no longer remember what's it called and/or it's been buried under more recent things so I can't find it*
Also sometimes it annoys me how frequently I use parentheses and dashes. I used 6 dashes in this post.