Sean:
You are asking a series of questions, each of which is complicated and none of which is best addressed via BB posts. It's hard to get full, complete answers to these questions even when talking at length with officials in the various countries (a bit of which I've done). Based on our 3 years cruising inside the EU, looking at the dual citizenship option (which I'm also eligible for), and hearing from a lot of other EU/non-EU sailors, my sense is that none of the info posted above is fully correct nor fully inaccurate. This is not because the other posters are ill informed but rather because all these topics depend a great deal on one's individual circumstances, the specific officials of the individual member state who are providing the answers, and the point in time when you face them - EU legislation is a moving target, Big Time, as are the understandings that local officials have and what local influences they are under.
Here are some specific answers I do have confidence in...tho' perhaps at the risk of violating my own cautions above.
1. Your USCG license will have no absolute reciprocity over here nor relevance. It might help you in certain circumstances, both official and in marketing, but it carries no specific legal authority of which I'm aware inside the EU. There's much detail related to this issue.
2. There is no direct correlation between how Customs/Zoll/Toll/Duane/etc. officials will treat your vessel re: VAT and how the Immigration/Polite/etc. officials will treat you as EU citizens; the two are totally separate. Similarly, you won't automatically be eligible to reflag your vessel based on your citizenship alone. E.g. if you wanted to reflag (for insurance, chartering or other reasons), you'd face the same new requirements as any other Irish citizen buying a new unflagged boat.
3. You will not need to necessarily pay VAT, and under current EU guidelines you can avoid it indefintely...if you want to keep the boat moving. OTOH if you want to set up shop in a specific locale indefinitely inside the EU, you may find paying VAT to be more desirable - at which point it can remain inside the EU without further VAT liability or geographic restriction. (For more on VAT see the article I wrote at
http://www.svsarah.com/Whoosh/Whoosh.htm And since you mention this as a 10-year plan, remember that the EU is slowly swallowing up almost all of Western Europe. Aside from the N African countries, most non-EU countries either bordering the Med (not counting the Middle East) are in process of seeking EU membeship status.
4. While EU citizenship MAY allow you to work, there is no guarantee that will be the case in a specific location for a specific type of work. General EU-allowed worker rights are further governed by the local labor laws in each country, let along informal local practice. Similarly, you may e.g. find no restrictions to setting up a charter company in the UK but find inpenetrable bureaucracy to doing so in Greece. The biggest single conceptual mistake we North Americans make when trying to understand the EU is to apply our view of a federal national govt. system to the EU; it doesn't work like that over here. Rather, it's more like the Confederation national govt. structure that the USA first set up before the Constitution was written. Moreover, the EU is still trying to figure a lot of things out...and as you can appreciate, implementation towards uniformity can take years even after EU agreement. To this already-dynamic state, add the impact of mostly poorer countries recently being added to the EU and you can see that it is a very hard environment from which to find iron-clad practicies.
5. Bureaucracy is one of the major products produced by most (not all) EU countries. I may sound glib when saying that but I mean it seriously. It provides immense employment, its viewed as a positive, constructive element in most societies (unlike how we regard bureaucrats in the U.S. as a necessary evil - or worse), and so this becomes a part of both the culture and the 'process' of living here. As stated in a post above, you therefore are much better equipped if you can deal with the locals in their own language, since their ability with English increasingly dissipates as a thorny issue materializes. This is independent from how much satsifaction and mutual appreciation one engenders when struggling with a bit of the local tongue; we are doing terribly with Portuguese right now (it looks like Spanish but sounds like Russian!) but everyone surely appreciates our efforts.
When you get to the right time in this plan, I'd encourage you to pick up the SSCA CD of previous Bulletins, wherein there is a great deal of information available on this topic, little of it totally consistent. I've also found official websites to be both very helpful and terribly inconsistent, and I've also found various officials in a number of countries to offer conflicting views. It's a tough nut to crack and my best advice is to consider it one of those intellectual tasks you'll never fully complete but, the more you narrow your focus to a given issue and for a given locale, you'll cement an understanding with the local folks that will be fairly clear and reliable (tho' not necessarily satisfactory from your point of view).
Accepting life inside the EU is an acquired taste, IMO - and often (tho' not always) quite a departure from the free-form, less regulated and entrepreneurial nature of life in N America. Along with many pleasures, of course.
For an excellent overview of cruising inside the EU, consider reading Walt Paul's write-up at the CCA website -
http://www.cruisingclub.org/ In fact, all his articles are well-researched and would be useful info for a charter captain who is assuming legal responsibilities related to GMDSS.
Jack