AFAIK you simply scroll into the map using the mouse whell, which spreads pins apart. :)
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Zoom in. Then the pins spread out.
So here's the thing, what are you using the pins for?
In the UM case, I'm using it so that I can track where the party is on the map, and what is near them. (Note the story title showing with the mouse over). I drop a "Party" token on the map so I can track them. Here's the map zoomed into a party location;
Attachment 25179
And then when needed I can open the linked story entry which then has the room description, boxed text, link to the locale battle map (a zoomed in high resolution version of the map), link to the encounter & treasure parcel, and as well as links to other story entries, rollable tables or anything else appropriate for that location. And, in my case I also include a note to the coordinates of the location, because the map is so large, if someone opens a story entry, this way they can reference back to the map and say 'ok, this location is in sector D6, let me go find it'.
Attachment 25180
So, in this case, I'm using the pins to get the info on the things that are in the area I'm interested in, and I know where the area is because that's where the adventuring party is.
But, if you want to look at a whole city map and know where all the blacksmiths are, or where all the city watch guard posts are, or other 'demographic' type of info, pins are not going to work well. That's where a color coded map comes in.
And from what I can tell, all the pins does not impact performance. After all, the pins are only a handful of bytes worth of information (coordinates). Opening that map takes something like half a second, and I suspect that's all because of the size of the image and not the number of pins.
Oh, the other suggestion I will say if you are populating something like this, create a story template that creates stories entries with a consistent layout. Maybe a few story templates if you have different types of entries you want. But, consistency is important for ease of use. Once people get familiar, all of your entries should have the same layout. For example, here's the story template I use for these entries;
Attachment 25181
I've mapped Waterdeep. It is a lot better than just paper, but it still wasn't fantastic.
This is my opinion, but I think that the best thing to do would be to dupe the map off and create maps with related types of businesses. For instance, a map will all the inns and taverns, another with all the armorers and potion makers, another with noble houses, another with guilds, and so on. Reduce the number of pins on map by pre-filtering the content.
EDIT: I am waiting to see what features FGU offers before I waste any time trying to work inside the current constraints of the FG engine. A big city map, frankly, will probably prove to be a huge waste of time once new features arrive. If the new version FG doesn't manage new map markers and layered images, I am going to be fairly disappointed. If the text engine doesn't have embedded image support, you guessed it, I am going to be somewhat disappointed. (Dynamic lighting was shown - a feature that I really don't want, need, or care about - but it sure sounds a lot more complicated than putting different colored pins on a map, eh?) So I am just saying, maybe you might end up getting across the finish line only to discover that there is another race in the offing.
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Ultimately Top - at this stage FGU is only advertising feature parity and similar UI/UX.
Achieving these things and backward compatibility are the primary 1st stage goals.
Once they are bedded down then feature improvements will start to happen.
That doesnt mean there will be no new features in FGU version 1 but it totally will not have all the bajillion things that people have expressed as their Unity wants.