Alignment, performance. 

1)Formatting issues
1)Linking Universes
1)hiding of variables you cant do it in xi r2

Before Migration, one should have a thorough with
1. Import Wizard
2. Report Conversion Tool - for converting the DeskI 
Reports to WebI Reports

Issues can be:
1. What type of Migration u want to Use-
a) Single Pass 
b) Incremental Migration

2. Importing Security or not.
3. Repository Migartion- such as 
a) Merging Multiple repository into one
b) Moving one to Multiple Repository (Depends on the 
requirement)
4. Need to take care of Versions and Platforms - Supported 
databases,Web and Application Servers, Web Browsers and 
Operating Systems.
5. User/Group Migration
6. Setting up Folders/Groups Structures.
7. Document Migartion.
8. Taking Backups
9. Setting Up Servers etc.

There are lot other issues also.