Connect your iPad or iPhone to your computer. I'm talking PC here. Click on either 'Computer' or 'Windows Explorer' and look for iPhone or iPad and click on it. In the window 'Internal Storage' appears. Click on Internal Storage and DCIM File Folder appears. Click on DCIM File Folder and in my case 11 or 12 file folders appear with names like 873SDNOQ. Note that these are called 'File Folders' not albums. Now what we are trying to figure out is why this brilliant operating system creates 11 or 12 folders to store less than 20 photos making it a pain in the ass when you try to find photos you have just taken in order to transfer them to an 'Album!'And if it was a computer thing why is it that when I connect my Canon Digital SLR to my computer I find all my photos in one album and don't have to go searching for them? It's definately an IOS thing.
Your comments triggered a few new thoughts. Luckily I have aspirin handy.
I haven't looked at the DCIM folder since the iOS 8 update, however it's possible things have changed and Apple is using some sort of folder structure to organize the photos now. The new Photos app organizes things by Moments. It also groups pictures if they are taken in multi-shot mode.
If that is the case, then deleting those folders would mess up how Photos is organizing things.
This is speculation. I don't know anything for sure, but it is consistent with how iTunes and Photos on a Mac store files; a complex direct access unfriendly sub-folder system. As with most file organization methods it's got plusses and minuses.
The plus is that the basic organization is inherent. You're not depending just on secondary files or metadata to keep things organized, so the database can be reconstructed if records get corrupted. The minus you are experiencing. Accessing those files directly becomes a nightmare.
Maybe I'll look into it further, to make sure this is what's happening.
At any rate, if you really need all your files dumped in the same place on the computer you have two (that I can think of) choices. You can use something like DropBox or another cloud service to export and keep the photos. Or, you can use a third party app like PhotoSync to export the photos to the computer, instead of accessing the DCIM folder directly.
Not great answers, but what I've got.
BTW, this is pretty much how it works on a Mac already. You can't see the DCIM folder on a Mac without installing special software. Instead you have a native app (Image Capture) that looks at the iPad (or camera), shows you the photos, and give you import tools. No messing around with direct folder access.