I actually agree with you when you think about messaging as a stand alone feature.  I look at it this way.  Secure messaging is just one tool I use when completing a fully independent Nxt transaction.  Meaning, at one point you will be able to browse products, communicate with seller, initiate purchase, put Nxt in escrow (receive item), send funds, leave feedback, all within Nxt client.  That is just one example of hundreds that could be used with Nxt secure messaging.

Messages should be used for technical staff and should be well-paid. 1.0

We are not talking about longterm. Right now no reason to lower fees because of messaging, because there is no use for messaging (chat).

Fee: 1.0
Until we really have high price for 1 NXT.
Until we really have big number of transactions per block.
Until we really start to scream: "WTF, I buy one gram of blow cheap cheneese smartphone and need to pay 5% of it's price as fee!"