Flexibility is the key if a new technology expects migration from an older one. In general, my recommendation is to leave the interchange in tact so that other communication mechanisms are not affected. In the long run, the trading partner will have some type of directory with trading partner information in it. One of the fields pertains to communication mechanism preferred. Thus, the initiating TP can look up the receiving TP in the directory, determine what type of communication method is preferred and route accordingly.
Flexibility needs to be left up to the TPs.
A similar argument goes for applying security. Again flexibility is the key. In its purest sense, I think you're right. We should recommend something for the Internet that will result in as little changes to the EDI application layer as possible i.e. minimize re-mapping and EDI translator adjustments for the switch to the Internet from VANs. Meanwhile, the best solution is to follow current X12 compliant enveloping for now.