One thing I think the Shapeshifter should have over any other is this:
When using the abilities of the Shapeshifter class, you *retain* your base physical abilities and adjust them with the racial modifiers of the new form.
I looked up Master of Many Forms on Google, and one of the first things I found was a thread on Wizards talking about strength and dexterity being dump stats. But hell, if you are a shapeshifter with no spell-like abilities, what the hell else are you going to want to put your stat points in to improve your abilities? Having your own strength, dexterity and constitution translate into the new form is, I think, integral to making it a good class.
Skills... hmmm... 6 + Int/level?
Balance, Bluff, Climb, Concentration, Craft, Disguise, Escape Artist, Heal, Hide, Intimidate, Jump, Listen, Move Silently, Profession, Search, Speak Language, Spot, Survival, Swim, Tumble
I left out Handle Animal, because the Shapeshifter is a master of shape, not making friends. Bluff and Intimidate make sense for wild animals, where Diplomacy and Sense Motive make less sense, at least in my line of reasoning. I was going to put in Knowledge skills, but instead, to make sure it covers only what abilities make sense, I would give them a Shifting Knowledge ability, like bardic knowledge, that gives them a bonus equal to their class level on checks made to discern the abilities of any creature. Synergy from the appropriate skills would apply, however.
One other thing I am not sure about... What creature types to you see a Shifter being able to take on? I see it as rather limited. Humanoids, Animals and Vermin to start, adding in Monstrous Humanoids, Magical Beasts and Giants as levels progress, and probably Fey and Abberations as well. Outsiders maybe as well. Constructs, Elementals, Oozes, Plants and Undead I'm less certain of. Elementals could possibly part of their normal progression, or Outsiders might not be, but Constructs, Oozes, Plants and Undead I think should require at least a feat chain, and maybe even a prestige class. I think I would keep Elementals and Outsiders as part of this group of special cases. My reasoning being that creatures of these types are a fundamental shift away from animal-like creatures to completely different kinds of life (plants), non-life (constructs, undead and oozes), and forces (elementals and outsiders).