My sense is that the Sega Master System II, the C64 GS, the PS3 Slim, and the Wii Mini are all disqualified because they lost too much. The Wii Mini was particularly bizarre as it lost a key feature in WiFi (yes, it lost WiFi!) while being only slightly smaller than the original.
Most of the other mini redesigns were smaller, lighter, and cheaper (to make, if not sold cheaper), and might even miss a feature or two from time to time (optical audio in the PS4 Slim, for example), but I believe most consumers would consider them functionality equivalent.
That means, to my mind, there are three with a credible claim to the throne:
Xbox 360 S: This was a big deal. It was a little smaller, but it was the model that signalled the end of widespread RROD problems (and anyone who lived through that era knows that was huge). It also was the first Xbox 360 model to have integrated WiFi, and the first one to go to a 250GB HDD for the deluxe model, and the first to have on-board flash storage for the base model. The Xbox 360 S was also the first model to not require extra cabling for the Kinect, back in a time when Kinect was promising and popular. The Xbox 360 Slim was a big, big deal.
Sega CDX (Multi-Mega in Europe): The Sega CDX was a premium product that few could afford, but that almost makes it more legendary rather than less. It was a Sega Genesis and Sega CD (or Mega Drive and Mega CD if you prefer), all in one. It cost more than buying the two separately, but added the ability to take it with you as a portable CD player. Compared to what it was replacing, I believe this one to be far and away the biggest size reduction of any official "slim" model.
Xbox One S: This is the only unit that is actually more powerful than the model it replaced. While it doesn't make a difference in every game, it does boast improved frame rates and less screen tearing in some titles. The total list of improvements in the Xbox One S is suprisingly long: HDR colour in supported titles, an IR blaster in the console itself, streaming 4K output, UHD, BD-XL, an improved controller (bluetooth, better shoulder buttons, longer range), support for being placed vertically, moving the power supply inside despite the size reduction, and all of that in addition to the 40% size reduction and the significant reduction in power consumption.
Those are the top three IMO in no particularly order. You can argue that the Xbox 360 S is the biggest reliability improvement (the build quality of slims are often worse than their original, but this one was better). You can argue that the Sega CDX was the biggest size reduction. You can argue that the Xbox One S is the only one to add power and has the most impressive list of added features. All three have a credible claim to the throne IMO, depending on what you find important in a slim re-release.