It's...stupid why people think Pokemon Trainer is among the first on the chopping block.
I mean, he's Red, the first Pokemon protagonist, and he brings something unique to the table with the switching out and the stamina mechanic. It may not work well in practice, but still.
I think the reason why people think he is low priority is because they feel like the whole switching out system is too hard or not needed.
I think his chances to stay are quite high, partly considering Pokemon Origins and how popular it got.
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It all has to do with development time. As Sakurai states, balancing is less of addition and more like multiplication. This character, not Red, Pokemon Trainer, has several unique mechanics that make him more difficult to actually develop (such as the stamina and switching out, as you mentioned). You have 4 models you need to animate, 4 voice clips, and you have to integrate him into every stage. Charizard represents everything Pokemon Trainer represents (minus the Trainer aspect).
Balancing Mario (a 3 time veteran).
Mario against the roster.
Balancing Pokemon Trainer (a 1 time veteran).
Squirt vs Ivy
Squirt vs Char
Char vs Ivy
Pokemon Trainer (Char vs Ivy vs Squirt)
Pokemon Trainer against roster
Squirt against roster
Ivy against roster
This also over-saturates the Pokemon series in comparison to Mario and Zelda (a little irrelevant, but it is the cherry on the top).