Hello from the future. The commit log doesn’t mention why it was deprecated, but whatyouhide, a core team member, explained a bit on this issue:

Elixir deprecated the usage of Enum.filter_map/3 because it was counterintuitive and the same could be achieved with Enum.filter/2 + Enum.map/2, with Stream, or with a for comprehension.

And also José Valim in the mailing list:

I would use comprehensions:

for item <- 1, 2, 3,
    rem(item, 2) == 0,
    do: item * 2

There is no reason for Enum.filter_map or Enum.map_filter to exist besides backwards compatibility.

Here is an example of using comprehension in lieu of Enum.filter_map/3:

# filter even numbers
filter_fn = fn n ->
  rem(n, 2) == 0
end

# double
map_fn = fn n ->
  n * 2
end

some_enum = 1..20

# filter_map version
Enum.filter_map(some_enum, filter_fn, map_fn)

# comprehension version
for n <- some_enum, filter_fn.(n), do: map_fn.(n)

Technically flat_map, like reduce are considered base-most enumeration functions. flat_map is the base-most that always returns another enumeration, and reduce is the base-most that returns anything. filter_map is pretty duplicative as I always use flat_map anyways.