Those are some nice options; I will throw in my two cents as well as add one additional place to consider:
Grace: This would be my first choice; I believe Grace has surpassed Alinea as Chicago's best restaurant. Top notch service that is highly polished yet personable, beautiful dining room that manages to be both elegant and comfortable and food that is artistically creative, interesting and most importantly consistently delicious.
Moto: This would be my second choice; Moto has undergone many changes in the past couple of years and has shown steady improvement; I have been dining here 4-5 times per year the past couple of years and each visit becomes a little bit better. Still some whimsy in their dishes, but they are focusing more on taste than wacky presentations. I recommend asking to be seating downstairs in the "lab" if you dine here; quieter more intimate space and one of the food prep areas is in the room so you can watch some of the chefs work as you dine.
Sixteen: Sixteen for me is boom-or-bust. I have been here a few times and both service and food quality has been wildly variable. I love that they totally change the menus with the seasons and it is a fun dining experience, but service has been off on three of my four visits and on all but one visit there were a few courses that just did not do it for me. The one visit where everything clicked though was truly fantastic. The current menu theme does seem like a cool concept and a friend recently dined there and had nothing but good things to say.
L2O: Good choice if you want a seafood centric food. My meals here have featured outstanding quality food from start to finish, but service - while extremely polished, is a bit impersonal and the ambiance is more old fashioned and formal than I prefer. Outstanding food, but not the best overall dining experience IMHO.
Acadia: Only been here once; it was not a very good experience, but in fairness to the restaurant it was a while back and they were fairly new at the time. I also had some friends have a subpar experience around the time of my dinner, but have been hearing better things of late. Am hoping to give them another chance sometime this year.
Senza: Not on your list, but something you should consider. They recently earned a Michelin star and their executive chef hails from Schwa. You see some Schwa influence in his food in that he loves to blend sweet and savory, but overall the food (style and presentation wise), ambiance and service style is similar to Goosefoot. You mentioned your wife loving Goosefoot best, so this might be another gem for her. I love Senza and find the food fantastic, the space comfortable and pleasant and service is very friendly (like Goosefoot) but not as polished at venues such as L2O. My only compliant about Senza (and Goosefoot) is the menu very rarely changes significantly - just little tweaks here and there. Not an issue for a first visit like yours, but for me the only thing stopping me from dining at Senza quarterly is the very slow changes to the menu.
Twitter: @Goof_2