Hi Zel! I'm Aquilae who wrote the SG5X walkthrough, if you don't remember.
Actually I would like to raise some concerns about the difficulty of 5X (I'm probably the only one who says it it easy =$), and some possible fixes.
First would be the downward curve in which the difficulty moves, as the pokemon gain EVs through battling and completely outshine the computer trainer's pokemon, despite the level difference.
That is why I was pushing for increased levels toward the end of the game, Carlos & Amelia (around Level 75 pokemon) were comparatively easier to beat even with their pokemon 15 levels higher than mine, and I found the earlier battles, Whitney and Bugsy to name a few challenging ones, actually were harder than Carlos & Amelia.
I would also like to see another change, that is a change in movesets as the game progresses, streamlining and improving throughout the game. In one of the posts you made you described the Elite Four rematch as having comparatively better movesets than the earlier trainers. Unfortunately I have failed to observe this phenomenon happening with the Gym Leaders of Beta Five, simply put the Kanto gym leaders have absolutely horrid movesets that fail to get past a wide variety of pokemon that counter it.
In competitive battling having a moveset that can handle several types/score super effective hits on a variety of pokemon is called the maximising type coverage, and generally helps in aiding the potency of the pokemon itself.
For example if Zapdos countered by Golem because Drill Peck and Thunderbolt are resisted by it.
But if the Zapdos had Hidden Power Ice, it would beat Golem and help with Ground types which come in to null Thunderbolt, increasing type coverage.
I have a lot of suggestions for the improvement of the Gym Leaders, I would be using Sabrina as an example:
Espeon lv 63: Psychic, Shadow Ball, Morning Sun, Reflect
Mr Mime lv 62: Psychic, Shadow Ball, Light Screen, Reflect
Alakazam lv 64: Psychic, Shadow Ball, Recover, Reflect
This team is 100% beaten by a Dark type, and a Psychic resister provided it isn't weak to Ghost. Shadow Ball draws off Espeon, Mr. Mime and Alakazam's comparatively lower attack stats, it won't be hurting much.
So how would a Psychic go around beating Dark types? For one, there is Medicham which possesses Fighting moves which are super effective on Dark.
There is another option in a defensive pokemon which uses Calm Mind, say a Grumpig, which could beat Dark types one-on-one given the Sp. Def boost Calm Mind provides and sweep an unprepared team.
You see, there are a lot of ways to fix the things that are lacking in the gym leader teams, which would make them even more difficult to deal with.
Granted, there are some parts of the game that are really difficult, I would say Whitney is one of the hardest.
Basically getting a Fighting type, most probably MUSCLE the Machop, would make it easier to deal with. Another thing that I have attempted to do is to use Butterfree's Sleep Powder, with its ability Compoundeyes, Sleep Powder has almost 100% accuracy and it incapacitates the opponent pokemon. I also have used Intimidate to my advantage as Miltank and Clefairy use only physical attacks - Intimidate lowers Attack which also weakens Whitney's pokemon.
I would not suggest an increase in difficulty in the earlier parts of the game, probably up till Whitney, but I would like to see an increase in difficulty, that is an increase in levels and better movesets toward the end.
I wish you good luck with Shiny Gold, and I hope you have taken the time to read my overly long message.