Firstly, __proto__ is nonstandard, and deprecated. If you write JavaScript that uses it, it won't run in all JS runtimes.
Object.create is similarly not available everywhere. It's not available in Firefox < 4, IE < 9, or any version of Opera. Crockford's version of Object.create is not compatible with the native Object.create -- and if you patch it in, you may end up breaking libraries that expect the real thing.
But let's say you had it all sorted out, and you had a sane plan for using the native Object.create, and falling back to Crockford's implementation where unavailable ... it's still not a great pattern:
http://jsperf.com/object-create-vs-crockford-vs-jorge-vs-con...
Running that again today, I see that in Chrome, instantiating objects via Object.create -- either Crockford's or native -- is over 95% slower than using a regular constructor function. We're talking about just creating basic objects here, low-level stuff: how fast you can do it is pretty important if you're aiming for high-performance JavaScript.
The prototype property, constructor functions, and "new" are the way that JavaScript objects work, and the way that engines are tuned to optimize JS code. Avoid learning to use them at your own peril.