Been using both since the early 2000s. VX1000 has the color I prefer, and the fisheye provides more bubble distortion (as the most available lens on the 21 is the mk2, which does not do the 180 degree field of vision the vx1 mk1 does). If you can find a VX21 MK1 fisheye it does have a bit more vignet.
As someone said, the 1000 is much more fragile. It even sounds delicate. You just need to maintain it (i.e. send it in for tuneups before it breaks - tighten the video circuit and clean the heads every 8-12 months).
There are a handful of advantages to the 21 - as mentioned, it is better in low light, but it is also better in variable light. Partial shadows and things like that can be tricky with the vx1.
For long lens, the zoom capabilities are also better with a 21 - the toggle has variable speeds (i.e. press down more = zoom faster). Once you get used to it, you can get more creative with long lens filming. The vx1 only has 1 zoom speed.
The 21 is also easier in setting your colors. With the 1000, what you see through the eyepiece is not what you get in the computer. I have basically gotten used to setting the camera the right amount of incorrect color/exposure knowing how it will ultimately look correct on a computer. The 21 is a little more straightforward.
21 also has a zoom ring, but that isn't really something I use.
With all of that said, I am a 1000 guy, even with all of it's shortcomings. Not to sound like a bandwagoner - you just can't beat the fisheye, and if I am going to use it for fish, I will use it for long lens as well for consistency. My vx21 is the most reliable capture camera I have ever owned!
Edit: when I say using both since the early 2000s, I guess I'm talking about the 2000 as well. 2100s were 2005ish I think. All the same facts hold true for a 2000 as a 2100 in regards to my comments above (with the exception of zoom ring? Don't think the 2000 has one).