If you are trying to have 4 scenarios, why does you script run the usage macro in three of the 4 scenarios (only moving on to the final two echo commands in your script if both options are present on the command line?

Please describe what you want your script to do in these 4 scenarios. Without knowing what these 4 scenarios are, I don't see how we can guess at how to correct your script.

And, what is the format of the -i and -e option-arguments. From your code I assume that the strings include: or exclude:, respectively, must occur somewhere in the option-arguments (not necessarily at the start of those option-arguments), but why these strings are needed (rather than assumed from the option-letter) is not clear, what else is expected in those option-arguments is not clear, and whether or not some default value should be used for these option-arguments if the options are not specified on the command line is not clear.

Please also show us an actual synopsis for your utility showing the utility name, the options, and operands that are expected in the various valid manners in which your utility can be invoked. (For example, the string -query appears at the end of your usage statement. Is that an indication that there are 4 more options (-q, -u, -r, and -y as well as a -e without an option-argument), or is it another mandatory string that is supposed to appear as the final operand to your utility?

You seem to have several operands that are required to be constant pathnames. Why does a user have to type in a constant pathname when your script could supply it automatically without the user having to type it in every time your script is invoked?