My new boat in EU, which flag? VAT reduced?

I don't know if a commercial yacht exists as a definition... If anything I would guess that is a Charter Yacht, as opposed to a Private Yacht (of course, a charter yacht could be used for private use, but a private yacht can't be used for charter legally). The charter licenses are usually more expensive and have stricter requirements to deal with safety and such...

Many of the countries with flags of convenience distinguish between commercial and pleasure classification in the registration of the vessel. It is my understanding that a commerically registered vessel is VAT exempt on fuel and certain provisions in the EU. However, there are more stringent inspection and safety requirements to contend with. The Marshall Islands allow a vessel to be non-commerical but accept up to 12 weeks of charter per year.

One of the real issues is what is your intened use of the vessel? Secondly does the vessel have ABS, MCA, or Lloyds classification? This should be what guides your choice of a flag. The VAT loop holes in bringing a boat into the EU exist regardless of the EU flag.

Yacht registration

Have a look at www.registerayacht.com

I worked together with them in the past and they will find a solution.

The right choose depends also on the home berth in case we have different
regulations in every land in the EU. Spain for example asked for a Spanish Charter Licence ( 12 % of the Yacht price ) In other countrys you have to sail
out of the EU every 182 days etc. So you will need professional assistance to find the right flag.