Trying to maybe bring something :
OP said to "connect the dots". When you connect the dots, it is in an alphabetical order if we talk about letters.
So I tried to with the tags :
But as you can see, It doesn't really represent something
And I tried ordering by name:
with those values:
Barcelona
Belgrade
Brest
Bucharest
Cologne
Frankfurt
Kiev
Krakow
Ljubljana
London Heathrow
Nice
Poznan
Strasbourg
Warsaw
Zagreb
Note that I took "London Heathrow" and not "Heatrow".
And as always, nothing comes to my mind when I see this.
This theory works with the fact that OP said that some of the tags were useless : " in order to have a prime number of stops"
There is only 2 duplicates in there : NCE & BEG:
And they indeed are useless if we order it by alphabet.
Another idea would be to connect them by the exterior (just like wrapping around them). But I do not have the time now..
I just tried to help and bring something. And sorry for the formating. Still learning how to use it.