I think the best restaurant I've visited in Prague has been the Strahov Monastery brewery. But as I peruse the Michelin list online, I realize that we have visited no highly rated restaurants in Prague in almost two total weeks there. So I guess we've been very happy in the run-of-the-mill places we've frequented, relying primarily on Google reviews. I love Slavic food, but even if one doesn't, Prague is a terrific restaurant city.
I will say that I'd avoid the Kolkovna Olympia. The only poor dining experience we had in Prague last summer. I'd also avoid Fat Cat for burgers and beers, not because the food is bad but because it's absurdly overpriced.