U Fleku is extraordinarily smoky and no Czech people go there (unless they are entertaining tourists). There are plenty of better dark beers. Might as well tick it off the bucket list, but I went once and will never go again.
Go to Pivovarsky Klub (about an hours walk from city center). They'll have 2-3 better dark beers on tap, a stunning bottle selection, great food (Bordain went there on No Reservations) and no smoking.
Pivovarsky Dum is owned by the same people, in the city center. It is a small brewpub with pretty good food. The regular light and dark beer (Czech people only call beer from Pilsen Pilsener, natch) are pretty good and the specialty stuff ranges from weird to weird but awesome. When I was there they had an almond mead that was awesome (not made there). If you see that on the menu, order a pour. They only do tours for groups.
You can get unfiltered Pilsner Urquell (Tankvar) a billion places in Prague, do so.
Everyone talks up Wenceslas Square. It struck me as a crappier version of Times Square (and I hate Times Square). Another place no Czech people in their right mind go. Much better places to hang out in Prague but, again, might as well go and tick it off the list.
If you go to Pilsen, hit up the Bernard tied house there (closed Sunday and Monday I think, check online). They are one of my favorite Czech breweries.