Exchange 200x clusters install in two separate phases: In the first phase, the administrator runs SETUP.EXE on the CD. The Exchange binaries are copied from the CD to the local harddrive, some IIS bindings are created, miscellaneous local-to-the-node stuff happens. A number of things are read from the AD, but little (if anything) is actually written to the AD in this step. After all nodes of the cluster have this first step run, the administrator moves on to the second phase. In the second phase of the install, the administrator fires up the Cluster Administrator interface (CluAdmin) and creates a system attendant resource. During this second phase, the Exchange Virtual Server (EVS) is created in the AD -- lots of writing to the AD.
The important takeaway from all this is that we don't create an Exchange server object in the configuration container during the first part of the setup process on Exchange 200x cluster, only during the second part.
And that leads to a minor difference between Exchange standalone servers and Exchange clusters. Since running SETUP.EXE on a non-clustered server will basically combine the two cluster setup phases into one big SETUP run, you have to make lots of decisions in the SETUP interface. I'm going to focus on the decision you have to make about what Admin group the server will join (if you have more than one). In a non-clustered server, you have to decide this from within the SETUP program -- BEFORE it ever copies the binaries.
Exchange Clusters, however, prompt you for that decision only during the creation of the System Attendant Resource. But it's important to note that underneath the covers, Exchange Setup still needs to have an Admin Group selected. It needs this even though it's not actually going to use it for anything but filler during this first phase of setup. What it appears to do is select the first Admin Group in the organization, alphabetically.
This can be confusing because if you read through the Exchange Server Setup Progress.Log file, it will imply that setup will be installing this cluster into some random AG in your org -- most likely one you don't want it installed into! But remember, it's not actually going to install it into the AG. Selecting the AG is a part of the phase 2 setup process.
Long story short -- if for whatever reason, the Exchange 200x setup (phase 1) on a cluster stops and prompts you for 5.5 credentials to join an Admin Group *AND* all the fields are blank and unchangeable, you now have the advantage. Knowing that it's simply trying to read the first alphabetical AG from the AD and is evidently failing in some way (permissions, problems talking to the 5.5 server directly, etc), an easy workaround might be to simply create a pure E2k/E2k3 AG through ESM and name it so it will be the first alphabetical AG in your org! Cluster will then read THAT AG instead, and voila, you're past the prompt and no worse for it.