I have an old American made 2EQ S.U.B. StingRay with a slab body and a StingRay Special, so I can't really compare with how the old 3EQ sounds, but I'll try to describe the difference between the 2EQ and the Special.
I think the biggest difference between the 2EQ and the Special is the amount of treble you can boost in the EQ. For good, or for worse, the old 2EQ has more top end and can thus sound much thinner, if you aren't boosting the bass.
The Special, to my ears, sounds more defined in the bottom end and isn't as aggressive as the old 2EQ, though it still sounds very StingRay-like. I think the new pre-amp voicing and the new pickups make the bass even more flexible than the old pre-amp. You can really tweak the sound a lot with the pre-amp and just the single pickup.
Generally, I think I prefer the sound of the Special, but at the same time I haven't bonded with the Special in the same way as my old 2EQ StingRay and I am not sure why. It might be the colour of the Special, or it might be because that the band I bought the Special for broke up shortly after I bought it. The ergonomics and weight of the Special are a an improvement compared to the old design. The Special I have haven’t got the slight deadspot that my old StingRay has around the sixth fret of the g-string either. Even though I prefer the Special I just play the 2EQ more and thus I am in the process of selling the Special. If I end up missing the Special, I might buy another one in black at some point as the Special is a great bass. It might be the simple (and expensive and stupid, haha) solution for me.
The two models look similar, but the ergonomics of the new Special models are improved, and the Special has a nice easy access to the higher frets and an extra fret too. My Special is light as it only weighs 3,6 kilo (or 7.9 pounds). Compared to my old, and somewhat light, StingRay which weighs 4,2 kilo (9.2 pounds), the Special just wins in comfortability. And I think the Special is the best bass that I have yet to play. It just plays really well.