I don't know if this game still has anyone's interest or not, but I have been working on some things after playing this game again and watching the latest WR run and thought that I would share some of the things that I have come across in case someone wants to tackle the game.
I have been wondering for a while if there was another Pokèmon that could be useful other than Feraligatr for the end game and the only one that came to mind was Entei. Now with Entei you lose the ability to use spread moves, but it is made up by being much faster and being a stronger attacker as well. Only thing is that Entei's strongest move, Fire Blast, only has 5 PP but fortunately there is a PP UP in the Shadow Pokèmon Lab to boost the PP for that.
In conclusion to all of this, I feel that Entei will probably be a better choice over Feraligatr because of its sheer power, despite the lack of spread moves, which are weaker in doubles, as opposed to having each Pokèmon using a single target move and hitting much harder with stronger moves.
Something else that I thought of is that Hidden Power will probably be needed to help with coverage for the last half of the game. I think that Espeon will need HP Ice and that Entei will need HP Ground. These round out a good amount of coverage, HP Ground can be used over Fire Blast against Steel types in certain places to maintain its PP, knock out fire types in the last sets of fights and take out all of the Magnemites, Magnetons, and Electrodes in the Lab, along with Ein's Lanturn/Raikou. HP Ice cleans up a lot of end game Pokèmon as there are a slough of grass and flying types along with dragons. The other reason that these Hidden Powers are picked the way they are is because this is a Gen 3 game and hasn't had the Physical/Special split, so Ground type moves are Physical and Ice type moves are Special, which is best used for each of their best attack stat.
I have made a guide for the IV's that will be needed for each Hidden Power, this is for Power 65-70, I feel like these are probably going to be the most relevant, for both Ice and Ground:
https://docs.google.com/spreadsheets/d/13x587VLWuqDPpFuFuVUQ_mAK5pKmE1rk_uwatDzOxAM/edit?usp=sharing
For those that don't know, I know that it is stated in the sheet but in case people don't look at it, IV's have a range between 0-31 inclusive, but for some Hidden Powers their respective cap might end at 30 in some stats for their 70 base power, which is the highest that it can go this generation (the only Hidden Power that can have all maxed IV's is Dark type.) This guide helps in the fact that it shows that you can keep the same power for the Hidden Power even if you have lower IV's which can be manipulated for certain situations. Like for Espeon, since it is a special attacker, you will want a high Special Attack IV, so you would either want 27 or 31 IV's, but maybe you would want to have a lower defense to influence what Pokèmon an opponent will send out, or maybe a slightly lower Attack IV since Espeon barely uses a physical attack, the only one that is used is Return.
Now for a full game route, that I don't have yet. I'm missing IV's and natures for all of the trainer's Pokèmon that aren't Shadow Pokèmon, would need to know if they are all consistent since that would help out with rounding out working on damage calcs for the whole run. The only thing that I have truly worked on a little bit on is the Ferma fight on top of the Pyrite building that you go to after winning in the Colosseum. We would want Croc to have a +Speed nature with 31 IVs in Speed to be able to outspeed her Mantine potentially.
That goes my next point is that I think that it would be wise to manipulate to not have Croc go into Hyper Mode since this locks you out of using other moves and healing after using Shadow Rush so much due to recoil.
Other than that the only other thing that I can say is that Shadow Pokèmon can have their IV's and natures manipulated, so this can lead to those Pokèmon being taken out a lot faster than normal by just giving them a low HP IV and then the corresponding defense stat a low IV with a stat dropping nature. For instance, referring back to the Croc vs. Mantine fight, a Croc with 31 IV's in Speed and a +Speed nature can outspeed a Mantine if it either has a neutral Speed nature it has 0-5 IV's to be outsped or 6-8 IV's to speed tie, or if it has a -Speed nature and it has 0-23 IV's it will be outsped or with 24-26 IV's it will have a speed tie. The reason why this is important is because we can use Bite and flinch the Mantine for a few turns while Espeon takes out Ferma's other Pokèmon(It would be preferable not to have a -Speed nature and have a -SpD nature instead so that Bite does more damage.)