I'd choose the 1Ds MkII, even over the 5D MkII, but it all boils down to what you shoot. In fact I did choose the 1Ds MkII, but I rarely go over ISO400, so the worse ISO performance isn't a problem for me.
That said, if you would be satisfied with the 5Dc, the 1Ds MkII is better than it in pretty much all areas.
The issue with going 1-series is that you don't want to go back to "prosumer" cameras anymore...
I don't find the ISO performance of the 1Ds Mark II as troubling as you say there.
I have also upgraded from a 450D to a 1Ds Mark II. At first I wanted it as a temporary camera, to get used to shooting full frame, weight etc. However, now it has a place in my heart and I know that I won't be able to kick it out of there. When compared, the 1Ds Mark II does of course kick the 450D's ass - that's the way it should be, right?
However, there are some points you have to live with if you go for the 1Ds Mark II:
- ISO, AF, MODE (all on the left of the top side) are pretty hard to setup - you'll need two hands
- Screen: it's pretty crappy. You need the feeling for the exposure (or stick with what the 1Ds Mark II tells you), because you really do not want to judge shots and their exposure from that small, reflecting display
- All the buttons and combinations: you'll have quite a time to figure out how to zoom in and move the magnifier in the picture. At least it took me some time, maybe it's just my stupidity.
Other than that rest assured it's even though discontinued a top tier camera which is capable of doing excellent shots. Here's my favorite shot (not retouched but sadly JPG only, I'll upload the RAW full size shot if someone's interested) I did with the 1Ds Mark II and the 16-35mm in a church:
If you want the camera to shoot and don't care about fancy menus, fast switching of ISO and screen, this one is for you.
If you can't live without these things, then get yourself a 5D Mark II.
Of course the camera has many pro points, but I won't take the time to list those as well. Either one is able to live with the negative points or one shall get a different camera.
By the way: I bought my 1Ds Mark II used for only $1300 at a local store with 1 year warranty. Battery is still amazing, I rarely have to charge it.