The biggest answer you gave, far and away, was the Game Boy Advance SP. I can’t say I’m surprised; no console before or since has been able to claim an improvement as big as “you can actually see the games you’re playing now.” Beyond that, though, the SP was really a superb redesign; it made the system less clunky to put in your pocket, and the buttons just felt better.
Of course, it seems fitting a handheld would inspire the most love here. After all, you have to actually hold the thing while you play games on it, which isn’t as much the case with consoles (though one person did specifically say the loved the first original Xbox controller over the second one). The DS lite (my personal favorite) got its fair share of votes, but not enough to compete with more popular systems.
As for the 3DS, it’s hard to quantify properly. Several people wrote in about the system, but between the 3DS XL, The New 3DS, and the 3DS XL (and the 2DS, which had as many votes as its screen has dimensions), the votes were split. Also, considering the names are often interchangeable (I know I often find myself saying “New 3DS” when I technically mean “New 3DS XL”), it was hard to know which specific iteration people were voting for. But let it be known many people think at least one of the updates to that system was their favorite.
A couple of people also loved the Game Boy Pocket, which I had completely forgotten about. A few also chimed in and said one of the PlayStation Portable updates was their favorite as well.
As for consoles, it was a close race. The Xbox 360 model S just barely etched out the PlayStation 2 Slim, with the PlayStation 3 Slim right behind it (very few people cited the Xbox 360 Model E or third iteration of the PlayStation 3 as their favorite). The Xbox One S got as many votes as the PSOne (which is to say, not many), though the console only recently launched.
From there, you have your smattering of older consoles; people like the second Super Nintendo model and quite a bit, a couple liked the Genesis redesign, and one person said they loved the 32X.
And that’s it! The GI community really loves console updates. Let us know if there’s any you think have been woefully overlooked.