if i were to have my choice between a Honda Civic SI, the generation I would choose is the 99-00.
Inexpensive, lightweight, with some safety features, nice suspension, proven engine, and plenty of existing aftermarket support.
however, I believe the 2002-05 SIs are a waste of a car. I like almost everything about the 06/07 SI Coupe, and for only 70 lbs more and matching numbers, the sedan does not sound too bad..
And I think honda is still manufacturing them as manuals because of the success they have had with their resale value in older cars (i.e. 90's-99, etc). More people buy manuals to build them up versus automatics. So, in about 6-10 years, when these cars are more available, and less expensive, and people start to build them up as project cars, the manual option is going to be more useful than the automatic. Why cut down manual production for the small % that may want an automatic transmission. This is why the standard EX Coupe/Sedan exists with the automatic transmission. The SI is performance-focused.