1) Add "overwrite" option to the Import Script dialog so it is not necessary to use the command line (Project.SSDTImportScript /FileName d:\temp\cots.sql /encoding Unicode /Overwrite true /IgnoreExtendedProperties true /IgnorePermissions true /AddImportedPermissionsToModel true) to obtain access to this functionality.
2) Add support in both Import Script and Schema Comparisons (from database to project) for supporting the more detailed folders (Keys, Constraints, Statistics, etc.) used by Database Projects and not just consolidating everything into the CREATE TABLE scripts.
As an alternative to #2, document this significant change in behavior for SSDT so this is not a surprise for the users and enhance the software that upgrades Database Projects to SSDT Projects to consolidate existing scripts of types that are now consolidated in CREATE TABLE scripts into the existing CREATE TABLE scripts to enable consistent handling of the scripts once the Project has been converted to SSDT.