Kinda like saying all cars are the same because they all have an engine and four wheels.
Each company uses Android as the base, kinda like the chasis of a car.
The hardware of the phone is like the engine, some phones have a great engine, others not so much.
The most obvious part is what each company does on top of the Android UI, also known as the skin. HTC has Sense, Motorola has Blur, Samsung has Touchwiz. Some do it right, some don't. None are as lightweight as a stock Android phone.
So looking at my analogy, the hardware is the car's engine, the skin is how heavy the car is. Doesn't matter if you have 300 HP, if your car weighs 17,000 pounds, it isn't going to feel like a powerful car.
Same with the phones. You can have great hardware, like the new Droid X2, with dual-core processors, but weigh it down with poorly programmed and heavy Blur, and the phone is sluggish and lags. Once the devs get in to the phone, remove all the unnecessary weight, and lighten the impact that Blur has on the phone, you will realize a huge increase in the phone's responsiveness and see that you really do have a nice phone underneath all that baggage.
So when we look at phones, we have to consider what's riding on top, Sense is pretty good, I actually like it. When I had a Droid X, I had to use a launcher on it, ADX just to get rid of Moto Blur as much as possible, and went ended up putting Gingerbread on it just to get the phone to live up to its potential.
Sorry for the long post, but I hope that I helped you understand why all Android isn't the same.