1. XI R2 has a 5 tier architecture,where as 6.5 has 3 tier
2. In XI R2 we have some new tools like Import wizard,    
conversion tool etc.
3. In 6.5 we have a product called Business objects but now 
its been renamed as Desktop intellegence.
4.In 6.5 we have supervisor, but there is no supervisor in 
XI and they have introduced the new concept of CMC which is 
used to created users,user groups etc.
5.In 6.5 reports are being stored in document domain of 
repository, now they have introduced the concept of folders 
and catagories.
6.In 6.5 we have BCA(broad cast agent)to schedule the 
repots but in XI there is no BCA, u can schedule the 
reports using "Scheduler" in CMC
7. not only these even in designer,deski&webi, u have some 
new enhancements

hi,
  WEBI Wise:--1) In 6.5 there is no "Alerts"
              2) In Boxi having "alerts & Sub Alerts" also

BOXI- Web Based Appliaction
BO 6.5 - Most of features are support only in Windows based 
application

In Business Objects 6.5 Repositories are created by 
Supervisor after installing the software, Where as in BO 
XIR2 by default 3 repositories are created while installing 
the software.they are central management repository,File 
repository and Audit repository.