I just wanted to update this thread with a solution that worked for me. I had a requirement to develop a replication client that would work with 2008 R2 and 2005 Full and Express editions (basically SQL 9.0 and higher).
I encountered the cryptic "Class not registered" exception for the MergeSynchronizationAgent early on and had the same problem some others have had where my dev environment is 64 bit and my deployment environments are mixed 32 and 64. The first fix to that was to choose Any Platform as the build type. That allowed me to get past the error when using 2008 R2 Full and Express editions. However, clients using SQL 2005 still got the same exception.
To fix that scenario I had to do the following:
Install the following 2008 R2 Redistributables from Microsoft:
SharedManagementObjects.msi
SqlCmdLnUtils.msi
sqlncli.msi
SQLSysClrTypes.msi
Not included, but required to use RMO was:
sql_rmo.msi
This will allow you get as far as creating a subscription successfully at the client, however, you will still encounter the "Class not registered" exception when you attempt to do anything with your MergeSynchronizationAgent.
To overcome that, I had to copy the entire contents of the COM folder from a healthy SQL 2008 Express installation to the failing 2005 client environment and register the following dlls manually using regsvr32:
cd "C:\Program Files\Microsoft SQL Server\100\COM"
regsvr32 AXSCPHST.DLL
regsvr32 mergetxt.dll
regsvr32 msgprox.dll
regsvr32 REPLAGNT.dll
regsvr32 REPLDP.dll
regsvr32 replerrx.dll
regsvr32 replisapi.dll
regsvr32 replprov.dll
regsvr32 replrec.dll
regsvr32 replsub.dll
regsvr32 sqldistx.dll
regsvr32 sqlmergx.dll
regsvr32 ssradd.dll
regsvr32 ssravg.dll
regsvr32 ssrdown.dll
regsvr32 ssrmax.dll
regsvr32 ssrmin.dll
regsvr32 ssrpub.dll
regsvr32 ssrup.dll
regsvr32 xmlsub.dll
At this point you should be able to subscribe and sync at your leisure using a 2005 host in 32 bit environments.
This cost me some time and frustration while researching, but I've learned much from it.
Hopefully this helps someone else...