Bots don't have limits. I've had 300 bots before. It lagged me like hell too. I'd say just allow 32 Brickmin at once. Just make sure the script is fast and smooth to reduce possible lag. Once you get further down the path on this project, I would try to Amade to help you with the bots.
Also, you might want to consider have a whistle tool. Seeing as it is a major tool in Pikmin the game, not having the whistle would be a bad idea.
Lastly, instead of throwing the bots, have to where you click on the bot, and it is added to your inventory. Then this item can be used to throw a 'dummy item', and where the item hits is where the bot spawns.