I have read about Lokal Dlouhá, and am planning a dinner there. Any other advice?
There appears to be an Asian inspired (but not particularly inspiring) place [Sansho] and a tasting menu place [Degustation] that get the most shoutouts for best food but don’t sound particularly great.
Happy to just drink beer and eat pub food - with the occasional duck meal - where is the best for that?
I would love that . And drinking the finest pilsners in the world :
It is Czech national food called Sviečkova, Duck is called Katchna.
https://www.zomato.com/sk/mikropivovar?bid=0&zref=collection
Is very nice restaurant.
[The above was written my cousin visiting from Slovakia. She will text her boss later, who goes to Prague often. Hopefully more recs soon.]. 
We ate at Sansho in '14 so I can’t comment on the current situation but it was SO wonderful at the time.
http://sansho.cz/#menu
CH is so freaking hard to navigate these days but found another:
I think this is the last one!
deluccacheesemonger (?sp ) loved Degustation but that was a few years ago. It was more than we wanted to pay at the time and too much food.