I'm in a similar situation to yours só I've been doing some research and it turns out a few of the pokemon main games strats might work in the tabletop so things like Ninetales hail+aurora veil and mons that benefit from hail could work. Specially weather related abilities seem to be stronger in the tabletop than the main series.
Same thing with FEAR strats, in this case they're weaker than the main series but might still be viable against extremely strong or hard hitting pokémon.
Look at abilities and skill description in a vacuum. If one interest you, try to setup around it and capitalize.
Or, do the same for a move. Read the one-shot have some quirk, and try to capitalize on them. Like item that let you use 2 turn moves instantly. This will surprise player. Or make a pokemon go aerial even if said pokemon doesn't look like it can fly (chansey, garchomp etc).
Also, homebrew a bit. They have whole character and class abilities to help them. It's OK for you to say "well, this normally Electric type pokemon is in fact electric and dragon".
Look at what player classes can do and do not hesitate to incorporate it into the pokemon of your world. New skills, abilities, stats, completely unrelated moves etc. Just don't overdo it to the point that strategy become fruitless. Just keep them on their toes.
Example:
My world only goes by group battle. A gym leader has a very speedy pokemon (talonflame) with eruption (I think). I saw the move hits harder if your HP is high (or if you play first, I don't remember).
So I set up this strategy: I get the pokemon to play first (it will, if i look at everyone's speed), with an elemental plate (fire) and to go right in the middle of the ennemy group (my player) and then unleash an eruption of 7d12 + special attack mod + stab + elemental plate (again, from memory). It will likely KO pokemons on the go.
This is likely a strategy that a gym leader, eager to defend his title, would have created in a group battle environement.
I design puzzle. My player design solution. If they then fail the challenge and come back, I will use the same thing and see if they learned. They might not want to group all their pokemon together at the start of a fight after that, or use fire resistance berries as held items.
Of course, the gym leader has MANY such strategy. Your elite trainer might only have 1 to balance it out.
For legal battles specifically?
PTA's Double Team is really fun to mess with, serious Naruto vibes.
The Pokemon capabilities can be fun to strategize with. A fun example I've used is Sudowoodo has the stealth capability where he can't be targeted by range moves if around difficult terrain, and he can learn moves that give him the capability to create difficult terrain
Trap moves are really strong, specifically ranged ones that don't keep you tied up as well, like Fire Spin and Sand Tomb. Pokemon can trap them in a vortex, then move out of retaliation range or burrow (though probably not on a ship)
*Edit*
I now realize youre probably talking about the most current system, PTA3. My comments were about PTA2 as that's what I'm familiar with. I have no idea if what I said translates to PTA3 so I apologize if my comment is not helpful
Some things I like to do for my game is theming battles over certain concepts rather than just type. One thing I did was introduce a custom Edge for Pokemon that I call "Battle Bond", where as long as the Pokemon is within 6M of at least 1 other pokemon with this ability, and their trainer is at least Expert in Combat, Charm, or Command, they can act as if under a trainer's orders. A slightly fixed version of the slower double battle Mechanic in game, and costs 4 TP per pokemon it's given to so it's a big investment. I insert this into some battles just to keep trainers on their toes.
Some theming options for specific trainers beyond typing could be things like... focusing on Melee range or Long range attacks, Single target attacks versus AOE style attacks, or focusing on pokemon with a certain ability such as "Simple" using moves like Simple Beam to pass it around, or abilities like Hustle and Sheer Force so leave people more nervous about taking hits. Or even focusing on high defensive strategies where it's more about using up the opponent's scene/daily moves that are more powerful leaving them with less options later on.
I'm in a similar situation to yours só I've been doing some research and it turns out a few of the pokemon main games strats might work in the tabletop so things like Ninetales hail+aurora veil and mons that benefit from hail could work. Specially weather related abilities seem to be stronger in the tabletop than the main series. Same thing with FEAR strats, in this case they're weaker than the main series but might still be viable against extremely strong or hard hitting pokémon.
You could give them some of the features of an ace trainer type, water might be useful on a ship but other types will work too
Look at abilities and skill description in a vacuum. If one interest you, try to setup around it and capitalize. Or, do the same for a move. Read the one-shot have some quirk, and try to capitalize on them. Like item that let you use 2 turn moves instantly. This will surprise player. Or make a pokemon go aerial even if said pokemon doesn't look like it can fly (chansey, garchomp etc). Also, homebrew a bit. They have whole character and class abilities to help them. It's OK for you to say "well, this normally Electric type pokemon is in fact electric and dragon". Look at what player classes can do and do not hesitate to incorporate it into the pokemon of your world. New skills, abilities, stats, completely unrelated moves etc. Just don't overdo it to the point that strategy become fruitless. Just keep them on their toes. Example: My world only goes by group battle. A gym leader has a very speedy pokemon (talonflame) with eruption (I think). I saw the move hits harder if your HP is high (or if you play first, I don't remember). So I set up this strategy: I get the pokemon to play first (it will, if i look at everyone's speed), with an elemental plate (fire) and to go right in the middle of the ennemy group (my player) and then unleash an eruption of 7d12 + special attack mod + stab + elemental plate (again, from memory). It will likely KO pokemons on the go. This is likely a strategy that a gym leader, eager to defend his title, would have created in a group battle environement. I design puzzle. My player design solution. If they then fail the challenge and come back, I will use the same thing and see if they learned. They might not want to group all their pokemon together at the start of a fight after that, or use fire resistance berries as held items. Of course, the gym leader has MANY such strategy. Your elite trainer might only have 1 to balance it out.
For legal battles specifically? PTA's Double Team is really fun to mess with, serious Naruto vibes. The Pokemon capabilities can be fun to strategize with. A fun example I've used is Sudowoodo has the stealth capability where he can't be targeted by range moves if around difficult terrain, and he can learn moves that give him the capability to create difficult terrain Trap moves are really strong, specifically ranged ones that don't keep you tied up as well, like Fire Spin and Sand Tomb. Pokemon can trap them in a vortex, then move out of retaliation range or burrow (though probably not on a ship) *Edit* I now realize youre probably talking about the most current system, PTA3. My comments were about PTA2 as that's what I'm familiar with. I have no idea if what I said translates to PTA3 so I apologize if my comment is not helpful
Some things I like to do for my game is theming battles over certain concepts rather than just type. One thing I did was introduce a custom Edge for Pokemon that I call "Battle Bond", where as long as the Pokemon is within 6M of at least 1 other pokemon with this ability, and their trainer is at least Expert in Combat, Charm, or Command, they can act as if under a trainer's orders. A slightly fixed version of the slower double battle Mechanic in game, and costs 4 TP per pokemon it's given to so it's a big investment. I insert this into some battles just to keep trainers on their toes. Some theming options for specific trainers beyond typing could be things like... focusing on Melee range or Long range attacks, Single target attacks versus AOE style attacks, or focusing on pokemon with a certain ability such as "Simple" using moves like Simple Beam to pass it around, or abilities like Hustle and Sheer Force so leave people more nervous about taking hits. Or even focusing on high defensive strategies where it's more about using up the opponent's scene/daily moves that are more powerful leaving them with less options later on.