[Is there a reason to do the Zygarde anomaly battle?]

From what I remember from my playthroughs, it's optional on the Lin route but compulsory on the Anna route. There's no point in doing it on the Lin route unless you want to.

[What does the ebony stonepiece do?]

12 minutes ago, Vulnona said:

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Well, I was wondering before... the first thing she says when she hits the ground is "you really are just like me". Those are the same words she says after she is beaten on Anna's path at the end of maingame. In his scene, Arceus pushes her off the edge and she falls somewhere. 

The Ebony cutscene just fits a bit too well to not be a continuation of this Anna's path scene... 

But then, I noticed that the dialogue really makes it seem like Lin and Arceus don't know each other yet (she thinks Arceus is just a noise, apologises for barging in, and calls the meteor a rock thing). 

... Puzzling! 

 

 

Spoiler

I'm assuming the idea is that Lin just happens to say the same thing to the doctor after he throws her underground as she does to Arceus at the end of Anna's path. It's definitely a confusing line of dialogue though so i'm not sure if that's the correct interpretation.

 

[What does the ebony stonepiece do?]

If you take the ebony stonepiece to the ruins beneath reborn city and enter the door at the top of the tower you get a short cutscene. As far as i know, that's all it does

[Zygarde Cell Guide?]

Here's the link: https://docs.google.com/document/d/1E25NCaVZkr_66C4pbMM-FANh0p7K-fBoJX0_ZP59ZPc/edit

 

There's 70 available but you only need to get 50 to get the ditto. Good luck

[General question about difficulty]

Souta is an absolutely massive difficulty spike even on casual. So, I can completely understand why you're struggling with it. Honestly the fight really needs to be made easier since the odds are just insanely stacked against you in that fight. To make matters worse, at that point in the game you're locked out of being able to EV train your pokemon easily. So, even if you did want to go through the trouble of EV training, it would be quite difficult. Instead of doing EV training and grinding, I would recommend to instead change the pokemon in your party and experiment with some different ones. Like you said, it might be worth thinking of some strategies.

One strategy you can do is use a team of flying pokemon so that you can take advantage of his overpowered field. For example, you can catch Talonflames in the area just before Souta's house near the train. Gale wings talonflame with acrobatics is extremely powerful in that fight. Also, if you happen to have an elemental seed, you can equip that to one of your pokemon so that your pokemon can get an automatic tailwind set up so that you can outspeed his pokemon and make it a little bit easier. Just make sure you save before fighting him so you don't waste the seed if you lose.

[Fun themes or restrictions for playthroughs]

One of my favourite challenge playthroughs was only allowing myself to use pokemon that were classified as untiered on Smogon. It forces you to use a lot of weaker pokemon which require more creative tactics to succeed in some of the fights. Other than that, a lot of people on this forum use monotype teams to make new playthroughs more interesting. So, for example, only allowing yourself to use dark type pokemon. There's also things like nuzlockes, but they're extremely difficult and frustrating to do in Rejuvenation and Reborn because of how the games are structured, so I wouldn't recommend them.

 

Edit:

Also I'd just like to add to this. Don't be afraid to take another break from the game until you're in the mood to try playing again. Reborn and Rejuvenation are extremely long, slow paced, and text heavy games. Like you said, it's very easy to get burnt out by playing them. I go through periods where I can't even get past the first gym without getting bored. But then I take a few months break, come back to play them again, and have a great time.

[Trick room?]

It's not a bug. It's in the real pokemon games too. The way prankster works is it increases the priority of a move by +1. However, trick room innately has a priority of -7 So, all prankster does is it makes is make trick room have a priority of -6. So, prankster trick room will still go last in almost every situation.