Telescopic Parentheses

x86 machine code, 39 34 33 30 29 bytes

00000000  68 c3 b8 07 31 ff be 82  00 b3 a0 ad 4e 3c 28 7c  |h...1.......N<(||
00000010  f0 77 05 ab 01 df eb f3  29 df ab eb ee           |.w......)....|
0000001d

x86 assembly for DOS, with some tricks:

    org 100h

section .text

start:
    ; point the segment ES to video memory
    ; (c3 is chosen so that it doubles as a "ret")
    push 0b8c3h
    pop es
    ; di: output pointer to video memory
    xor di,di
    ; si: input pointer from the command line
    mov si,82h
    ; one row=160 bytes (assume bh=0, as should be)
    mov bl,160
lop:
    ; read & increment si (assume direction flag clean)
    ; we read a whole word, so that later we have something nonzero to
    ; put into character attributes
    lodsw
    ; we read 2 bytes, go back 1
    dec si
    ; check what we read
    cmp al,'('
    ; less than `(`: we got the final `\n` - quit
    ; (we jump mid-instruction to get a c3 i.e. a ret)
    jl start+1
    ; more than `(`: assume we got a `)`
    ja closed
    ; write a whole word (char+attrs), so we end
    ; one position on the right
    stosw
    ; move down
    add di,bx
    ; rinse & repeat
    jmp lop
closed:
    ; move up
    sub di,bx
    ; as above
    stosw
    jmp lop

Limitations:

• it always prints starting at the bottom of the screen, without erasing first; a cls before running is almost mandatory;
• the colors are ugly; that's the consequence of recycling the next character as color attributes to save two bytes here and there;
• the code assumes bh=0 and the direction flag clear on start, both undocumented; OTOH, bx is explicitly set to zero in all DOS variants I saw (DosBox, MS-DOS 2, FreeDOS), and everywhere I tested the flags were already OK.

J, 32 28 bytes

This was a fun one.

0|:')(('&(i.-<:@+/\@i:){."0]

Explanation

This is how this solution works, including an explanation of how it has been golfed.

   NB. Let a be a test case
   a =. '((()())()(()(())()))'

   NB. level alterations
   _1 + ').(' i. a
1 1 1 _1 1 _1 _1 1 _1 1 1 _1 1 1 _1 _1 1 _1 _1 _1

   NB. absolute levels
   +/\ _1 + ').(' i. a
1 2 3 2 3 2 1 2 1 2 3 2 3 4 3 2 3 2 1 0

   NB. adjusted levels
   (+/\ _1 + ').(' i. a) - ')(' i. a
0 1 2 2 2 2 1 1 1 1 2 2 2 3 3 2 2 2 1 0

   NB. take level from end of each item of a and transpose
   |: a {."0~ _1 - (+/\ _1 + ').(' i. a) - ')(' i. a
(                  )
 (    )()(        ) 
  ()()    ()(  )()  
             ()     

   NB. code as a tacit verb
   [: |: ] {."0~ _1 - ([: +/\ _1 + ').(' i. ]) - ')(' i. ]

   NB. subtractions pulled into the prefix insert
   [: |: ] {."0~ (')(' i. ]) - [: <:@+/\ ').(' i. ]

   NB. i: instead of i. so we can use the same string constant
   [: |: ] {."0~ (')((' i. ]) - [: <:@+/\ ')((' i: ]

   NB. get rid of the caps
   0 |: ] {."0~ (')((' i. ]) - ')((' <:@+/\@i: ]

   NB. join the two usages of ')((' into a single dyadic phrase
   0 |: ] {."0~ ')((' (i. - <:@+/\@i:) ]

   NB. bond ')((' and flip arguments to {."0
   0 |: ')(('&(i. - <:@+/\@i:) {."0 ]

Retina + Bash, 27 bytes (14 + 10 + 3 = 27)

This makes use of ANSI Escapes:

\(
(\e[B
\)
\e[A)

Equivalent to sed -e "s/(/(\\\e[B/g;s/)/\\\e[A)/g". The \e[B escape code means move cursor down one row, and the \e[A means move cursor up one row, so this solution simply inserts those codes after and before the start and end of each nested pair of parentheses. Input is passed through STDIN.

You'll have to call it as printf $(Retina ...) to see the output correctly.

Output

(((())))
(\e[B(\e[B(\e[B(\e[B\e[A)\e[A)\e[A)\e[A)
^C
amans:~ a$ printf "(\e[B(\e[B(\e[B(\e[B\e[A)\e[A)\e[A)\e[A)"
(      )amans:~ a$ 
 (    )
  (  )
   ()

((()())()(()(())()))
(\e[B(\e[B(\e[B\e[A)(\e[B\e[A)\e[A)(\e[B\e[A)(\e[B(\e[B\e[A)(\e[B(\e[B\e[A)\e[A)(\e[B\e[A)\e[A)\e[A)
^C
amans:~ a$ printf "(\e[B(\e[B(\e[B\e[A)(\e[B\e[A)\e[A)(\e[B\e[A)(\e[B(\e[B\e[A)(\e[B(\e[B\e[A)\e[A)(\e[B\e[A)\e[A)\e[A)"
(                  )amans:~ a$ 
 (    )()(        )
  ()()    ()(  )()
             ()