Clearly parenthesize APL trains
APL (Dyalog Classic), 71 68 65 63 bytes



0{⍵≡⍕⍵:⍵⋄⍬≡⍵:'⍬'⋄1=≢⍵:⍺∇⊃⍵⋄3≥≢⍵:⍺⌽')(',⍣⍺∊1∇¨⍵⋄⍺∇¯3(↓,∘⊂1∇↑)⍵}⍎


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The characters I chose for I/O are '(', ')', and '⍬'.

This solution is itself an APL train.

⍎ parses the input as if it's a nested array - a tree with empty numeric vectors (⍬) as leaves.

The dfn (i.e. lambda - { }) traverses the tree recursively and converts it to a properly parenthesised string. The left argument ⍺ controls whether parentheses should be added to the current level if necessary.

The dfn handles the following cases based on the right argument:


if it's already a string (⍵≡⍕⍵), return it
if it's ⍬, return the char '⍬'
if it's a singleton, just dig deeper (∇ is the symbol for a recursive call)
if its length is ≤3, recurse for each of the items and surround with () if necessary
otherwise, recurse for the 3-tail, prepend all but the 3-tail, and recurse again