Well, TAC is very likely correct here - this is almost certainly an Exchange issue with messages not being pushed to their proper home store in a timely fashion.
In 2.x ALL messages (sub to sub or outside callers) are delivered in much the same way (i.e. there was no UMR queue in 2.x as there is in 3.x and later) - Unity creates the message in the mailbox of the sender addressed to the recipient. In the case of outside callers it's left in the "Unity Messaging System" mailbox created by setup.
At that point it's up to Exchange to deliver the message to the appropriate home store of the recipient via the MTA just as if you'd have logged into Outlook and left the message - Unity, in fact, uses some of the same connectivity mechanisms that Outlook clients do.
I'm guessing this is outside callers and that that Unity Messaging System account is the only account on the local Unity server - all other users are "off box". I'm further guessing that there's likely an MTA/RPC issue at play between the Unity server's Exchange and the external exchange servers - this is often a DNS issue. Check the event logs on the local Unity server and see if you find any RPC bind or bind-back errors, this is a common source of such a "delayed message delivery" problem report.
Short story, there isn't anything Unity 2.x could be doing on it's own to cause such delays - we don't hang on to messages and push them ourselves, they're created directly in Exchange and left for it to handle the delivery - if a message is eventually getting to where it's going it's a near certainty that it's an Exchange MTA related issue of some sort.
