Probably the best info I've seen on Med cruising is contained in the Cruising Club of America's pdf file at this address.
As far as visas and vats, we've been cruising the Med for the last 5 years and have yet to run into any issues. During the summer we keep moving and try to respect the "Schengen" 90 day limits. Of note; we have never been told or asked about it during a check-in or out.
We've spent three winters in EU countries (Greece, Malta, Spain) and make it a point to break up the 6 month winter stay by flying back to the states for 6-8 weeks. This has worked for us.
The only country we needed to be very careful about was Turkey (non-Schengen) they will issue you a visa that is good for 90 days (not three months) and will definitely fine you, if you exceed that. Most people get by this by a quick trip to Greece.
VAT now with the 18 month temporary importation you have plenty of time to restart your clock by visiting a non-EU country. Morocco, Tunisia, Turkey all come to mind. Again we have never been asked about the VAT status of the boat, but have also never pushed our luck by staying over 18 months.
Hope this helps you. You will absolutely love Med cruising. We started with a 6 month plan to see the Med in 2001 and are still here.
lying Andratx, Mallorca, Spain