Well there is one solution to this problem but it is very time consuming.
I use a program called YRoute along with TTools. After collecting the flight route info useing TTools go to the Flight Route word document and delete all of the info listed and save the empty document (this deletes all default routes) then go into the Aircraft document and add all of the aircraft you want to use and airspeeds. Then go into YRoute and go to the settings. change the Aicraft, Airport, and Flight Route folders to the word documents you just changed. Then go back to YRoute main menu and choose Load Defult Flight Plans. Now your ready to set up flight plans. use the Add Button under the top window to start. Select airports, aircraft, and flight times. You might want a list of airport codes. after you have set the routes you want click Save Flights on the right hand side and exit out of YRoute. Now go to TTools and compile all of the new plans. you should now have only planes you specified flying the routes.
You can find YRoute here:
www.spacejock.com look for it on the left column.