I just bought my CX-5 after wanting the CX-3. It is to replace a lease-end Mini Countryman All4, so the AWD was top most priority for the car. I like the more modern feel of the CX-3, since it is a new car. The CX-5 was only slightly updated, so it waasn't really redesigned for 2016 model....just updated from older years.
As for storage, yeah, the CX-3 is a penny racer. The CX-5 is an SUV! You have more leg room, and hella big cargo area. The CX-5 also has a shorter front end than the CX-3 (which is one stupid reason my wife immediately said NO to the CX-3, even though the CX-5 was on the bottom of her list due to the overall size. HA. *sigh* )
As for handling, without taking both out again, obviously the CX-3 will be peppier and lighter feel. it's a hatchback!!! The CX-5 is a much larger car. I did like both, that is for sure. I do miss my turbo though
The engines don't sound as nice as the Mini did.
Most options are the same really. Speakers are speakers. I LOOOVE LOVE LOVE the Bose sound. I've never bought a car with upgraded sound, so I'm HAPPY I got it. I listen to mostly all EDM, so i can tell, while there might not be a sub in the CX-5, it's freaking amazing compared to my Fit or the Mini. So, take that as you will.
I do not like the fact that the CX-5 has no digital Speedo. The CX-3 had one, AND it has the pop-up display thing, which was really neat. Again, the CX-3 was newly designed for this year, so there are more modern looks/features.