There are health schemes for most breeds - most large breeds for instance have issues with hips and elbows, there are schemes to screen for that before breeding, some breeds have hereditary eye or heart problems, again there are already schemes for that.
I don't think that's usually an issue - in that, some of these hereditary problems are more common in certain breeds, but they're not exclusive to them. Joint problems seem to be a size thing rather than specific breeds, eye problems are tested for in loads of breeds, poodles and labs for instance have the same eye issues (which is why labradoodles are problematic).
Good breeders, no matter what they're breeding for should be doing tests for whatever issues are relevant.
KC assured breeders have to, but apart from that, unfortunately it is voluntary.
So, no I don't think with most breeds it is a case of the best of a bad lot, GSDs with sloping backs work, the current crufts best of breed has working titles, I don't particularly care about a particular colour becoming fashionable, like paler retrievers, unless it leads to something more sinister.
But, with breeds with particularly exaggerated features I think it's different, things that affect basic functions like breathing - that's where I think there's an issue. No amount of screening for health problems can fix the fact that by exaggerating flat faces dogs can't breathe or by breeding for wrinkly skin they get eye problems (shar peis for instance are really bad for that).