You are right to point out that apps normally leave their configuration plist etc. in place when they are removed, and I do appreciate the obsession some folks have with having a "clean" installation. But with the restrictions Apple put around IOS, that is not always possible...
Where I think you are slightly mistaken is the amount of space such files take up. Even installing and removing hundreds of apps, the config files should be very small indeed. There are typically only a few kilobytes each.
The misconception really stems from what "other" data is all about. As I have posted elsewhere, "other" is not to be feared. It is NOT worthless data for which you should be on a mission to remove. Typically, most of the "other" data is made up of supporting data required for your apps, but the primary "culprits" are normally Photos, Music, Videos, and other media intensive apps.
When, for example, you synchronise photos onto your device, the iPad will create thumbnails for the photos and organise the meta-data into database files. These generate significant amounts of "other" data. It is unavoidable, and as I say, not to be feared. Without it, the apps simply don't work properly. You may also get significant amounts of "other" from the data which apps download, such as magazines... I have several magazine subscriptions in Newsstand which have many GB of data.
I would be extremely surprised if the "other" data which is related to your uninstalled apps is any more than a few tens of megabytes in total size. Do you have any evidence that there is significant amounts of irrelevant data "stuck" in your backup? How large is your backup? Do you store it on iCloud or iTunes?
If the backup is on iTunes you can use something like iBackupBot to interrogate it on your PC (free trial available - google it).
If it is on iCloud, what do the statistics say in the Settings app, about the backup size and content?
As an example, my "other" is currently over 4GB in size, but my backup on iCloud is around 450MB.