I haven't found the pods to be that bad in the rain. Granted, in a heavy downpour when you come to a stop, the bike may run rough and want to stall unless you keep it going with throttle blips, but once underway, it seems the rain blows by and the bike runs OK. Now, this is with side covers installed, totally open with no covers might be a different thing.
This is the only down side I've found to running pods, but I think the pluses far out weigh it so I'm willing to put up with it. I don't ride in the rain very much (if I can help it, lol) so it's mostly a non-issue for me.