The VSL interface is very limiting for an organ, but then it was presumably designed as a general-purpose orchestral instrument player rather than be too instrument-specific. As it stands, it's not too bad if you want to play something that uses fairly conventional registrations so you can set them up in advance as a custom matrix, but for anything else that either uses complex or "unconventional" registrations, or simply for improvisation, it's really not much use. One workaround that I'm experimenting with is the use of multiple instances of VI within my sequencer, all run off the same MIDI channel. Each instance has a small custom matrix that starts with an empty slot and contains stops of the same pitch. That way I can build up registrations by selecting the appropriate combination of 16', 8', 4' stops, etc. on an instance by instance basis. The next step would be to dust off my copy of MfxScript to simplify the selection of matrix cells and so I can use a midi controller device to select stops easily in the same way that I would if I were sitting at an organ console.
All of that said, the overal sound is wonderful. Maybe the wind pressure is a little low to successfully carry off some of my favourite 20th century French organ works, but for most of the symphonic organ repertoire it should be superb. Certainly a more organist-friendly interface would be nice, but so too would be the 12 stops of the Fernwerk. And the pedal Fagott and Bassethorn stops. And the Vox Humana with tremulant because that's how it's supposed to be played (although I can see the technical difficulties there). Oh, and the Glockenspiel [;)]