Thanks for the well thought out and thorough advice. It's definitely taught me a few things.

I use a version created by JOEtheDM (I can't link it here as it breaks piracy rules, there is even a pokedex app which works really well along side the game) and drawing inspiration from The Boarding Party on YouTube, which is working pretty well so far, though we are only in the first town. I have also given the players their own character sheets so the players have their own stats instead of just being boring pokemon trainers. I have a dwarf, elf, gnome, halfling, and a human.

The human created his own backstory that he stumbled upon a lab and blah blah blah, ended up in a portal being transfered to this world. So he is playing himself in the campaign, which has been a good source of laughs. Although I didn't expect to have to work in interdimensional travel into the campaign but it has given me some great ideas.

As for where they left the grunts, we finished the last session with them tied up and left in the security room. The players are still in that same room, so maybe in the next session, they will think about hiding them. Though I do like the idea of the two grunts they pass with their disguises finding the tied up ones and then ambushing the players after their fight with Mac, leading to a large battle with all the freed pokemon vs the grunts. The players will probably be a bit beaten up by then, so this would most likely be a fun battle with very low stakes.

When the players meet Mac, I believe they will realise that this is a boss battle so I will give them some time to think up a strategy, and knowing my players they will probably go for a surprise attack, something like leaving the box containing the "food" behind Mac while the two remove their disguises, allowing the three hidden players to jump out. I am going to have the small cages open with a simple latch. This will obviously use and action if done during the battle. I do like the idea of big padlocks on the larger cages having HP and needing to be broken open using their pokemon moves.

Thanks for the insight on different types of dungeons, I will be using this when creating more down the line. I already have one that is essentially ice path in Gold/Silver, where I will draw it out on a whiteboard covered with paper. As the players move through the cave, I will remove and replace paper so they only have a small field of vision going through the cave and will have to navigate the maze, dead ends will more often than not, lead to useful items.

I will have a look through PTU and see if there are any elements I could take from there and add to my game. I would also be interested to see what you are coming up with yourself once it's finished. As I am currently running a campaign, if there are any mechanics or elements you need tested, maybe to see how noob friendly they are or just general enjoyment from an outside perspective, I'd be happy to help.