Only other thing is, do you specify class names explicitly in "persistence.xml" ? If not then it will have to scan the classpath below the persistence-unit, hence taking some time to find the classes to load annotations for. The log info you provide doesn't show if it is this that takes the time - the log at debug would likely help.
Either way, i'd suggest you raise an issue on http://code.google.com/p/datanucleus-appengine/ so its registered
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