No expert in stone work speaking here, but we just had a flagstone patio & walkways installed and there is about 1.5-2 inches between the stones (less in some spots). We have mortared installation, no groundcover. However, it almost sounds like your installer was trying to skimp on the stones, but in fairness maybe he misunderstood what you wanted to do. If you are using groundcover, what type are you using, how rapid is its growth, and how do you expect to use the area (lots of walking on it or not, mowing over it or not, for example).

Sorry I missed your June 23rd deadline, but I ran into a similar situation. I bought enough dinnerplate and smaller sized pieces of 2" or so thick sandstone (obviously, I don't know the specific stone terms yet)to fill in a triangular shape leading to a gigantic rose arbor I built. I left a gap of 4-6" between each stone, thinking it would fill in nicely with groundcover. For some reason, I've always liked Gold Dust Alyssum, so I planted it between the stones. In the middle, however, I selected a low-growing sedum. Well, in no time, the Alyssum grew up and all-but covered the stone. When it bloomed and died back... well, let's just say it wasn't the effect I was after. So choosing the right plant to use between the stones is key.
I'm going to reposition the stones, leaving little, if any, gap between them. Obviously, I'll need more stone, or I can plant groundcover off to each side.
By the way, putting the stones and the groundcover in an area that served as my only way from the house to the shed was a BAD idea. I hated to roll a wheelbarrow over the stones and plants.
If one learnes from one's mistakes, I should be teaching by now.

Hyperboy.

Wouldn't it depend on the size of the flagstone and the size of your natural walk step? Mine are about 15" steping stones, (not flagstone) and mine are about 1 1/2" to 2" apart. That is a natural step for me to take on all the 14 stones.
Sky~~

My husband put in our flagstone walk. On the top he filled in with stones. The steps leading to the driveway, my Mom cut strips of Irish moss and put them between. They've grown in nicely and are a beautiful deep green and now have delicate white flowers. A greenhouse I frequent has a line called "steppables" groundcover that will take foot traffic. Kinda cool. I have some kind of thyme variety, they have filled in very well too. They aren't between stones but I would be happy with either the Irish moss or the steppables there.