Until the release of the Pokemon Trainer amiibo, the character of Pokemon Trainer was only represented by the Charizard amiibo, who was the only character of the trio that was playable in Smash 4, and thus received his own amiibo. Every Pokemon Trainer submitted to tournaments prior to the release of Pokemon Trainer was actually a Charizard amiibo that now functioned as Pokemon Trainer.
Pokemon Trainer is a very unique amiibo for a few reasons. First, he is represented by four different amiibo: Pokemon Trainer, Charizard, Ivysaur and Squirtle. Scanning in any one of these four will result in the same character, Pokemon Trainer, being used. Second, depending on which one was scanned in, the amiibo’s starting character is different. Scanning in Charizard requires that Pokemon Trainer start with Charizard in battle. Scanning in Ivysaur requires that Pokemon Trainer start with Ivysaur in battle, and so on. Scanning in the Pokemon Trainer amiibo allows trainers to select which starter is the first one out, which works in similar manner as choosing moves for Mii Fighters.
Pokemon Trainer is a unique amiibo for one more reason: all three characters share the same data. If you teach your Charizard to use forward smash to KO, then that same data applies to Squirtle as well. Functionally speaking, when Pokemon Trainer is in battle, every time he switches he is effectively brain transplanting a Charizard into a Squirtle into an Ivysaur and so on. The game doesn’t quite know how to properly handle this, so it gives Pokemon Trainer an affinity for switching often. Not only does it switch after each stock, it also makes the amiibo use Pokemon Change fairly often. Even if an amiibo trainer avoids using Pokemon Change during training, the amiibo will still use it occasionally.
This all demands the question: who should my amiibo start with?
It’s generally agreed upon in the community that Charizard on his own would be an S tier competitor, or at least high A or A+ tier. He’s heavy, hits like a truck, and has a good recovery. If he retained Rock Smash from Smash 4, then he’d be unstoppable.
It’s also reasonable to conclude Ivysaur would probably be around B tier on his own. He’s also heavy, has notably fewer moves that pack a hard punch, but still has some, and has a useful tether recovery. While he’s a bit weak on stage unless his opponent is directly above or below him, Ivysaur is a good fighter in his own right.
Squirtle exists, unfortunately. I’ll just attach a screenshot of the June 25 update to the amiibo tier list to explain Squirtle.
Squirtle is incredibly light and combo-based, making him optimal for human play. For amiibo play, he’s entirely worthless. His only knockback-based KO moves are up smash and Withdraw, which are difficult to land with but still quite useful. He’s the dead weight on Pokemon Trainer. On his own, Squirtle would likely be D tier.
So we’ve got a great character, a good character, and a dismally bad character. Considering that the changes go from Squirtle to Ivysaur to Charizard and back to Squirtle, who would be the best character to start with?
Squirtle, or Ivysaur.
Ideally we want to spend as much time as possible using Ivysaur or Charizard, our two usable characters. However, the AI likes to change Pokemon at seemingly random times. This means that whoever we start out with probably won’t be our character for very long, unless some training method is discovered to keep Pokemon Trainer from ever switching.
Taking this into consideration, and knowing that Squirtle can’t take a lot of damage while Ivysaur and Charizard can, it makes sense to start with Squirtle. He’ll either take enough damage to have to change early, or string together a few hits and then switch out automatically.
Starting with Ivysaur is also a good idea, but if the Pokemon Trainer decides to switch early, you’ll be minimizing your time spent on a usable character and instead spending more time with Squirtle.
The biggest factor in all of this is how often the Trainer changes. If it changes often (which it shouldn’t do, because that leaves it vulnerable) then it doesn’t matter as much who they start with. If they never change, except after losing a stock, then that’s still not good, as 3-stock matches mean they spend an entire match as Squirtle. Somewhere in the middle is the key, and that’s why it’s so difficult to determine exactly who Pokemon Trainer should start with.