The difference comes from the size of your company. The requirements for each are:
- Not named on more than 4 previously filed applications
- Gross income on last years tax filing does not exceed $150,162
- Under no obligation to assign/grant/convey a license/ownership to another entity that does not meet the income requirements.
- A nonprofit organization OR less than 500 employees
- Have not assigned/licensed/conveyed an interest in the invention to a non-small entity
Large entities pay the heights fees at the USPTO. There are no qualification to be a large entity. If you do not qualify as a micro entity or a small entity you are a large entity.