I've been obfuscating code in the same application since .Net 1, and it's been a major headache from a maintenance perspective. As you've mentioned, the serialization problem can be avoided, but it's really easy to make a mistake and obfuscate something you didn't want obfuscated. It's easy to break the build, or to change the obfuscation pattern and not be able to open old files. Plus it can be difficult to find out what went wrong and where.
Our choice was Xenocode, and were I to make the choice again today I would prefer to not obfuscate the code, or use Dotfuscator.
