I’ll pretty much always take a special over a jr. I use the neck pickup as much or more than the bridge and I like neck binding so they’re more my speed in general. I chose Les Paul over the sg body shape, but that’s just marginally my preference, I love and have/have had both.
Not to be a GC shill , but ... GC has the 2018 Classic Player Plus on sale at $1599. I got mine last Black Friday for just a bit less than that, and that was a Black Friday deal so $1599 is a great price -- they won't last. The guitar comes with HSC, neck/body binding, AA top, and titanium saddles. It comes with black trim and knobs which I recently changed out.
I asked myself the exact same question After really giving it some thought and playing as many as I could I went home with a Les Paul Special. I needed a neck pickup and between it and the SG there was just more of something, well, special about it.