There's a ton of segmentation going on in the iPad line. I think you've gone through the decision tree pretty well. To answer your question I think the last bit mostly comes down to a combination of price and what the retailer even has stocked and displayed - they may only have the latest one.

I agree the mini 2 and 3 are a little too close spec-wise. I think Apple is trying to figure out supply chain choices there, and the A7 is just a good chip that still has legs. I'd guess the consumer decision on that one would be if the consumer likes the form factor and wants the latest, they choose the 3, and if they look a bit more into it and find the 2 is just lacking fingerprint and they don't care, they choose 2. Most people aren't pouring over specs, and may not even know the 3 has the same guts as the 2.

More generally though, having this year's and last year's model in both form factors makes sense for price segmentation. It's doubly good for business as it clears out the supply chain, and it even suggests to purchasers that older products will be supported so you can have confidence in your purchase.