The Bean Factory is where you can upgrade your mechros by using the Beans you collect during a match. The number of times you can upgrade each of your mechros is based on your upgrade limit. With every level you gain, your upgrade limit increases by one. So if you are level 5, you can upgrade any of your mechros 5 times. You can also increase your limit by purchasing upgrade bonuses at the item shop.

Ice Time - decreases the frozen time from the Ice Cube.
Fire Resist - decreases the damage from Fire Cubes and exploding Item Cubes.
Critical - increases the chance of a critical hit from the blast punch.
Scale Time - increases the duration as a giant mechro and reduces the time as a tiny mechro.
Transform Time - increases the duration as a super mechro and reduces the time as a toy mechro.