I traded by 98 Prelude for a 2001 R, I dont regret it, not even for a second. I think if you have to debate the issue with yourself, you dont want an ITR.

As for the other issues, I am sure they are basically equally reliable. Both are great engines.
Theft is definitely a concern for R owners, as is vandalism. Also, it seems to make other drivers act like morons, revving at you all the time! It gets so old having people want to race you/show off all the time. I never had a single person do that to me in my Lude!