I once swapped Ctrl and Alt and never looked back. It feels so natural and it happens to match Symbolics Space-Cadet Keyboards layout too http://xahlee.info/kbd/space-cadet_keyboard.html

Advised by http://xahlee.info/kbd/linux_swap_modifier_keys.html

    ! -*- coding: utf-8 -*-
    ! 2013-02-04 swap Alt and Ctrl http://xahlee.info/

    !  xmodmap -pke | egrep '(Control|Super|Alt|Menu)'
    ! keycode  37 = Control_L NoSymbol Control_L
    ! keycode  64 = Alt_L Meta_L Alt_L Meta_L
    ! keycode 105 = Control_R NoSymbol Control_R
    ! keycode 108 = Alt_R Meta_R Alt_R Meta_R
    ! keycode 133 = Super_L NoSymbol Super_L
    ! keycode 134 = Super_R NoSymbol Super_R
    ! keycode 135 = Menu NoSymbol Menu
    ! keycode 147 = XF86MenuKB NoSymbol XF86MenuKB
    ! keycode 204 = NoSymbol Alt_L NoSymbol Alt_L
    ! keycode 206 = NoSymbol Super_L NoSymbol Super_L

    clear control
    clear mod1
    keycode 37 = Alt_L Meta_L
    keycode 105 = Alt_R Meta_R
    keycode 64 = Control_L
    keycode 108 = Control_R
    add control = Control_L Control_R
    add mod1 = Alt_L Meta_L