Unfortunately, the answer to this question isn't tied directly to a specific message size, but rather, depends on specific bottlenecks in your Microsoft BizTalk Server 2006 system. The problems associated with large messages can be divided into the following categories:
The original message size, message format, and type of message processing all affect how BizTalk Server processes large messages.
Follow these guidelines to improve performance when processing large messages in BizTalk Server:
HKLM\Software\Microsoft\BizTalk Server\3.0\Administration\TransformThreshold
Batch Size * Average size (in bytes) of each message in the batch after being processed by the receive pipeline < Large message threshold