Hi Victor, it's been a while
I never used CRI but I used to use CRII and CRE pretty extensively. I found the program pretty much indispensable, particularly for the online help and the character generation.
My biggest problem was that I used to use all the Player Option rules and even CRE didn't support them completely. Using the program always involved a lot of workarounds and the kind of customization that you could do was often pretty limited, even with the extension. I was also not terribly fond of the linear approach to character generation. E-tools' ability to jump instantly between different screens is a great improvement from a user interface point of view. As is the multi-window approach.
CR II scored best with the help feature. Having the books online with a fully-indexed help system was hugely useful. E-tools is catching up with this, I understand a lot of the text from the books will be added soon, but it's way behind CR II on that one.
CR II scores over e-tools with its ability to stow equipment in specific locations and the character sheets were pretty flexible, if I remember. The fact that the e-tools character sheets are output in XML is a plus for e-tools, however, especially for programmers like me who can mess around and customize them. Having the database accessible in Access is also very useful from a customization point of view.
I think with the latest 1.4 patch to E-tools, the customization available even without accessing the database, is light years ahead of CR II and with ET Helper you can even create classes (something that was a huge hole in CRII functionality, I recall). The support of the splat books through the new datasets is also much more complete with e-tools now that CMP have taken over and tentative dates from CMP reckon that the 3.5 datasets should be available within the month.
CR II was prettier than e-tools with its animation etc. but I think that from a user interface point of view and from a flexibility point of view e-tools definitely has the edge. Of course without the success of Core Rules WotC may never have agreed to commission e-tools so I don't really see the programs in competition. E-tools is just the next step on the way to the perfect character generator and with CMP at the helm things can only get better
Regards
Thrombin