The JBDS 2.0 Beta should include the latest EAP 4.3 instance. A decision has to be made if it is:
EAP 4.3 CP03 Still has Seam 1.2 Support or
EAP 4.3 CP02_FP01 which adds in Seam 2.0 Support.
Rich Sharples might be someone to engage to find out his opinions on this and the right choice.
I would think that CP02_FP01 would be the right choice.
If that is the case then the correct Seam version should be selected in the Seam New Project wizards.