Migration Assistant only allows selection of the entire Applications folder in part because some applications install support files, typically stored in the root level Library folder, that may or may not have any obvious relation to the application bundle in the Applications folder. To further complicate things, some apps share some of these support files. Application installers sort this out, making sure the correct versions of the support files are installed in the correct locations, but since different developers do this in different ways Migration Assistant can't know what belongs to what, so it takes an all or nothing approach to make sure the apps remain functional after migration.
For somewhat similar reasons, Migration Assistant does not let you arbitrarily pick & choose individual user folders to migrate (although it does allow you some choices). For example, if you select a specific user account to migrate, it will always try to migrate that account's ~/Library folder to insure that all per user application support files are transferred. But it will allow you to include or exclude certain user folders like Movies or Pictures, since these folders should have nothing in them that some application depends on for functionality.
It is actually a bit more complicated than that, since Migration Assistant does check things like version numbers to make sure it does not overwrite a new application version with an older one & it may be programmed with some information about Apple's own apps that allows it to make some choices it can't safely do for third party ones.
So the bottom line is if Migration Assistant's choices are to broad for your needs, you will have to try to do what it cannot & make sure you transfer all the necessary application support files along with the apps you want to transfer. Since this is not an easy task, it is generally better just to reinstall the apps on the new computer & let the installer take care of all that stuff.