OK I can give some suggestions with Mystic:
We like to go to John's Tavern for an afternoon beer. You can walk from the Seaport or dink there because it's just south of the bascule bridge on the east side across the park. Ask for a Black and While and watch the skilled bartender, who I know by at least three different names, sweat as he pours it. It has a way Irish atmosphere. They have a pool table and local characters and sailors hang out there.
Lattitude 41 has a good menu but is a little pricey. But it is a nice dining room and right there at the Seaport. I would call it New England Cuisine. Think chowders, cranberry breads, codfish, scallops etc.
We lightened up on the S&P Oyster Company after being seated upstairs in the family section. It was very noisy and the food was average. My wife loves Mystic Pizza but it is a tourist trap. You couldn't give that pizza away in Brooklyn. I haven't eaten there but I think Angie's pizza may be the real deal with regard to the movie.
The Engine Room for some mechanical atmosphere and craft beers after John's is our regular route. The menu features burgers. Best Bourbon bar in town.
There is a Mexican place on the west side of the bridge after the left turn on Noank Road. For me Mexican is Mexican. There is not good or bad. Well I guess there's bad.
There is the Captain Daniel Packer Inn for New England Inn Atmosphere and food.
There are a few places in Mystic Village which are OK for fried food or burgers but not really dining. Up by the highway there is the Steak Loft with a salad bar and Go Fish which is sort of a cafeteria atmosphere. There is also the Hilton, which had an award winning chowder a few years ago. They aren't listed as a restaurant at present on iMaps. But that chowder was really really good.
There are a couple of more high end restaurants in town that we haven't eaten at because they seem too expensive. So you're on your own there. So there's a lot more and that's not even counting Stonington, New London or the casinos. Don't rule out Lobster in the Raw at the entrance to Mystic River and/or the clam bar next door. It may be worth your time to spend a night in that Noank Shipyard, on your way in or out of Mystic for a lobster dinner and chowder. You'll want to do take out and eat on the boat to avoid the breeze in the PM that will too quickly cool your dinner. It is picnic table style lobster eating. You won't go hungry in South Eastern Connecticut.