First I want clarify that you should uninstall the previous version of RSAD otherwise Installation Manager will prevent you from progressing. After uninstalling you will also have to remove C:\Program Files\IBM\SDP (the location where you installed RSAD) or else Installation Manager will stop your progress. You should also keep track of any Eclipse plugins you have installed (like MercurialEclipse and TestNG) because you will probably also have to reinstall them.
After your installation your desktop shortcut might still contain "C:\Program Files\IBM\SDP\eclipse.exe" -product com.ibm.rational.rsa4ws.product.v95.ide in the Target field. I recommend changing it to v96.
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If you're running WAS 8.5 you will probably need to set your Compiler compliance level to 1.6 since it defaults to 1.8. This is unnecessary if you have IBM SDK 8 installed or are using WAS 9. You can find the setting in Preferences->Java->Compiler.