To clarify @Gray Lady, the red/green system would be at your final destination. In your case, the flight from one European airport to another (exception if LHR) is essentially domestic, so no Customs if you connected in MUC, or LIS, or FRA, and claimed your bags in BCN, for example.
As mentioned, its Immigration only. Customs is incredibly easy...red/green system. If you have anything to declare, you go in the red line. If you don't, you simply walk out the "green door" or exit door.
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This is always a risk when using cruise line airfares. The cruise line will put you where they can get the best fares, especially when doing a promotion involving a free flight. They are under NO obligation to get you the flight you think is best.
We always book our own, as do many people here.
I am going to speculate that winds AND seas may not have been the same. We have sailed through 70+ mph at least once (I think twice, but memory is fading) and slept right through them.
You can do an estimate on the Uber website. There are several shuttle services mentioned here...you can look at their websites for fares. Taxi is probably going to be in the $60 range.
Plus, I don't think there is a wide variety of service there, in terms of flights from a lot of places, so it doesn't really come up as an option for many to efficiently fly there.
Best in what way? All in one vehicle? Check some of the shuttle companies frequently mentioned here to do a private charter. Possibly a limo might be able to handle your group, but luggage is a question.
Cost? Use 2 or 3 Ubers. Even a taxi is cheaper than the transfers.
It's done frequently on the same cruise line, and discussed on the Alaska board regularly. It's called a B2B (back to back). Doing it on two different cruise lines is less commonly done, but it has been done. It's called a S2S (side to side).
The other option is to do a 14 day cruise on a cruise line like Holland America, where you will see probably 8 or 9 different ports, and probably 2 glacier days. A whole lot more of Alaska.
Try asking over on the Northern Europe board, here:
https://boards.cruisecritic.com/forum/116-northern-europe-amp-baltic-sea/
Several local residents that have knowledge. The hotel will hold your bags. You are just a couple blocks from most of the sights, including Tivoli.
There have been many discussions on the topic. You can upgrade only on board, and BEFORE you buy your first beverage on the plan. I don't know the current cost...I think its about $10 per person per day.
Currently...next month, Thalys no longer is a single train from Amsterdam to Paris. You have to connect in Brussels. Not sure how that might affect you. Not a big deal...60 minute connection. This appears to be a recent change.