Complicated list slicing

list = {{1, {x1, y1, z1}}, {2, {x2, y2, z2}}, {3, {x3, y3, z3}}};

In addition to your current method

{#[[1]], #[[2, 2]]} & /@ list 

You can use a number of additional methods, including

Transpose[{list[[All, 1]], list[[All, 2, 2]]}]
{#, #2[[2]]} & @@@ list
{#, #2 & @@ #2} & @@@ list
Transpose@Extract[Transpose[list], {{1}, {2, All, 2}}]
list2 = list; list2[[All, 2]] = list2[[All, 2, 2]]; list2
(* or, more simply, list[[All,2]]=list[[All,2,2]] if you want to modify the list *)
list3 = list; list3[[All, 2, 0]] = #2 &; list3

to get

{{1, y1}, {2, y2}, {3, y3}}

I find extracting the parts and then combining them (e.g. with Transpose) to be fast and general. kguler already showed this but again for reference:

{list[[All, 1]], list[[All, 2, 2]]}\[Transpose]

{{1, y1}, {2, y2}, {3, y3}}

Pattern matching is another general method, though often not quite as fast.

Cases[list, {a_, b_} :> {a, b[[2]]}]

{{1, y1}, {2, y2}, {3, y3}}

Since your example only requires modification of the {x1, y1, z1} part you could also use MapAt:

MapAt[#[[2]] &, list, {All, 2}]

{{1, y1}, {2, y2}, {3, y3}}

Using Replace

list /. {a_, b_List} :> {a, b[[2]]}

or

Replace[list, a_List :> a[[2]], {2}]

{{1, y1}, {2, y2}, {3, y3}}