Minor thing, but in Gen 1 you got the Silph Scope from the Rocket Hideout in Celadon. Aside from gameplay requiring you to do it before Sabrina, there wasn't any compulsion to go to Silph Co. in the games.I like Origins when it started. It gave me what I was looking for, an adaption of the game. Yes I understand things change between adaptions and I'm okay with that, it's just when they start going too off track I start having a bit of a problem. For example I have no problem with Brock giving Red advice before arriving to Pewter City. It feels like something a Gym Leader would do; like Brock was on a stroll when he noticed two trainers battling, saw mistakes Red did resulting him losing, so after the battle Brock goes up to Red and gives him some advice. It not only provides Red with a lesson to help understand why he lost but also sets up Brock as an experienced trainer so when its revealed he's a Gym Leader he just doesn't feel like a guy just created to be a boss. Heck I have no problem with the "over" focus on Charizard because its Red's Starter. I don't know about all of you but my main Pokemon is usually my Starter.
So at the start I was liking it... then those straying away from the story started to happen. First off Red not needing to go to Silph Co. to get the Silph Scopes to go through Pokemon Tower. Now I understood why they did it and for the Pokemo Tower story it works... problem is they still needed Red to get involved with Silph Co.. So if Red wasn't going to Silph Co. to get the Silph Scopes how was he going to get involved? Well they have a secretary escape Silph Co. with Red and Blue's help who explains Team Rocket took over. Okay, I guess that works but this sounds more like a situation for the police. Like with Pokemon Tower people were too afraid to go in due to the ghosts, but here this is a hostile takeover which is something the police can handle.
But wait! We gotta have Blue act like a jerk and not want to help which I felt was taking his character trait way too far. Blue is a jerk, yes, and he does see Team Rocket as a more of a nuisance than a real threat. But still I don't think he would just walk away going "not my problem", I'd more imagine it would be "Red, this isn't our responsibility. I'm getting the police". You can then have Red argue there won't be here in time so he's going in but still it would actually make Blue look better and honestly more reasonable.
But yeah, felt that getting Red into Silph Co. felt a bit sloppy since they changed the original reason he went there.
I also had no problem with Mr. Fuji giving Red the Mega Stone (though its a bit too coincidental how he just so happened to have a Charizardite X and Red's Starter was luckily a Charizard. Actually if anything wouldn't Mr. Fuji have a Mewtwonite?). It was meant to advertise the new games so whatever, and now if they did ever remake Gen I again we now know when we'll be getting the ability to Mega Evolve in those games. :P
Then we come to Viridian Gym. Oh boy, Viridian Gym. So first off Giovanni using one Pokemon and it being a RhyHORN is BS. Not a Rhydon, but its pre-evolution. And it then goes to knock out five of Red's Pokemon despite them using moves that have a type advantage and it using moves that aren't (the above mentioned Thunderbolting Jolteon. Jolteon knew Double Kick but that didn't do anything to it). What was wrong with a "full" battle? Just montage it and make sure to show Giovanni getting into the battle and remembering when he became a trainer. Also I'm not so sure how I feel about Giovanni's "redemption". On one hand it makes more sense why Giovanni would dissolve Team Rocket and want to start over as he was reminded of his passion for being a trainer. But on the other hand now the storyline for GS doesn't make quite as much sense (it could still work I suppose, but they would need to rewrite it as Origin's Giovanni has no reason to return to Team Rocket so it wouldn't make much sense for them to beg him to come back). Also once again Giovanni started out with a Charmander, really? What was wrong with giving him like a Nidoran male (I personally always say Nidoking being his signature Pokemon because NidoKING).
I really had no problem with the Mewtwo fight, maybe Red could have used all the Legendaries Birds and have them put up a decent fight but hey they have to advertise Mega Evolution so whatever; still resulted in a cool fight (and I liked Origin's Mewtwo Theme). Also they confirmed Mr. Fuji was responsible for Mewtwo's creation which was neat.
As far as the Giovanni battle, my one issue is that its progression is kind of contradictory to what Giovanni's arc seems like it should be. Giovanni became complacent using Pokemon as tools because no one could stop him, as shown when he curbstomped Red at Silph Co. That's sensible. So why does Giovanni's whole perspective on Pokemon change over the course of a battle that he's still dominating? Have Red legitimately give him a run for his money, and Giovanni remember what a thrill it was to have a good battle. It'd also coincide a bit with meshing his two motivations to end Team Rocket: Besides remembering why he loved Pokemon, it also shows he can better himself as a trainer, and Team Rocket isn't the way to do it. It stays in line with the Gen 2 plot since the Grunts might understand the latter, but not the former.