The problem with Gestalt is that if both sides give the same feature, you only take it once. A gestalt Ninja//Spellthief does not have 1 level of Ninja and 1 level of Spellthief, he has 1 level of Ninja-Spellthief.

Now, if you take a level of, say, Fighter//Rogue at 1st level, then take a level of Ninja/Rogue, then continue levels of Ninja/Rogue, you'll be getting Sneak Attack or Sudden Strike +1d6 at every level, because the levels you get sneak attack in rogue are the levels you don't get sudden strike, and vice versa.