I've been enjoying this game a lot so far, and I am looking forward to seeing how this develops in the future.
There are a couple things I noticed, however.
For one, you can buy any prestige upgrade multiple times, including one time upgrades like the target closest upgrade, which does nothing when bought more than once.
Rip 10 prestige points, you will be missed...
Additionally, the target closest, at least on my last session on 1.1.0, did not work correctly.
Instead of aiming at the center of the enemies hitbox, it seems to pick a random offset each game start, leading to it sometimes targeting an enemy and never being able to hit it, because the offset is way off from the actual hitbox.
Now for some suggestions;
Since you mentioned deeming the bug of the mouse up event listener not triggering upon leaving the game's container a feature in your reply to EndermanFran's comment, perhaps you could consider adding an auto shoot option to the settings menu?
I feel it would be a great QoL and accessibility feature, as well as allow you to do other things simultaneously (i.e. writing a comment for your game), as in the current state, any mouse click will trigger the event listener, thus halting any shooting.
Another feature I would personally love, is a new Prestige Upgrade, which speeds up the Gameplay in some way.
Especially the last two areas would benefit from this, given they can take quite some time to clear, and failing close to the end of area 12 can be very frustrating because of this.
Lastly, I would propose a way to Export and Import your save file.
The way you would currently need to do it, if you wanted to for example back up your save, is copy the Base64 data from your browsers Local Storage and then overwrite the value of "PokemonIncremental.0.html5game/gamedata.json" to import a save file.
Given the game's alpha stage, being able to easily export and import saves may be beneficial, as bugs (like the aforementioned prestige point theft that target closest does) are very likely to mess up save files.
The game is certainly headed in a great direction, and I do enjoy it a lot for what it is already.