Apple’s new flagship phone, the iPhone 5S, follows in the grand tradition of the iPhone 3GS and iPhone 4S. It offers subtle, almost imperceptible changes on the surface, and a complete brain transplant underneath.

While I can’t pretend to truly know the iPhone 5S –- we had maybe 45 minutes with it, total –- I can tell you that the transplant appears successful.

The Apple iPhone 5S clearly has some real power (a new A7 chip) and

At first glance, it’s quite easy to mistake the iPhone 5S for its predecessor. At the Apple launch event, I saw several instances where someone picked up another person's iPhone 5, thinking they were handling the new phone. The impression doesn’t last long. First of all, there’s the color. Apple's two new metallic finishes — "space gray" and gold — have an almost indescribable pop to them.

There are two other external differences. One is pretty subtle and the other is, as I see it, a pretty big deal. The first is the LED flash, which is actually two flashes. Called True Tone Flash, these two LEDs are designed to ameliorate the effects of odd lighting (like fluorescents) on flesh and colors. In my limited time with the phone, it was hard to tell how effective this is.

The second change is the iPhone 5S home button. It’s in the exact same spot as it was on the 5, but something is missing: the square. You know, the one with rounded corners that’s been on every iPhone since they were launched in 2007 (it’s also on iPads and iPods). That change is a signal of something new and momentous underneath the hood.

Apple’s introduction of a built-in fingerprint reader was a poorly-kept secret. Still, the execution is impressive. Touch ID uses a microns-thin sensor under the home button’s sapphire glass, just above the tactile sensor. First it remembers your fingerprint (thumb or finger), then reads it when you want to unlock the phone. I tried this out twice, and was impressed with how smoothly it went.

Touch ID uses multiple passes to analyze your print. It advised me to repeatedly place my finger on the home button, and that I shift positions so it could get a complete read. You can watch it build the reading with each pass. With my thumb and index finger, the process was the same. Once it was done, I was able to store a name for my fingerprint.

You can store multiple fingers. On one phone, both an Apple employee and I were able to log into the same phone using one of our two registered fingers.

It takes 20 seconds or so necessary to register a finger. Logging in makes that time well worth the effort. You press the home button and hold it while it reads your finger. This happens in less than a second, so it feels like you’re simply pressing to unlock the phone.

Apple is storing the encrypted ID information at a hardware level. That’s just how it should be done. Touch ID will be a significant selling point for the new phone.

Another significant change is the new iSight Camera. Apple updated both the build of the camera and the brainpower behind it. The new A7 chip (which also stores that encrypted security data) gives the camera all sorts of tricks, many of which brought to mind an expensive DSLR. The camera now starts analyzing the scene almost as soon as you hit the camera icon.

It can do an exposure grid, auto image stabilization and even adjust exposure in real-time on a panorama shot. What Apple did not do was engage in the megapixel race. While some smartphone manufacturers are touting 13 and even 41 MP cameras, Apple stayed at 8. Instead, the new image sensor is larger and actually accommodates larger pixels.

In a panorama shot of the demo room, which happened to have a large bright window, the iPhone 5s was surprisingly adept at auto-managing the exposure as I shot. Instead of an over-bright window with shadowed figures in the foreground, I got all the room detail. In a standard still, this would not be impressive. But in a panorama, the exposure is constantly changing. The iPhone 5s figured it out.

Burst mode worked as advertised. I shot 20 or more shots by simply holding down the shutter button. The iPhone 5S collected all my shots and automatically identified the best-exposed and (to an extent) best-composed shots. We also tried this with a photo of my face. To test the iPhone 5S's ability to find good facial expressions, we shot a burst mode of me looking serious, smiling and then sad. The phone highlighted the best — which were indeed the best — and then I had the option of selecting those for inclusion in my film roll.

Slow motion is a powerful feature that also lived up to its billing. The feature is one of the camera options. You can shoot your whole video in slow-mo and then, with an on-screen slider, choose which portions run at normal speed and which show off the 120fps shooting skills of the iPhone 5S. We tried shots with me waving. Each time, it just worked. Slow motion looked great on the iPhone screen.

There is quite a bit about the iPhone 5S I could not test. First of all, the phone is now a fully 64-bit device. This will give the phone more power — and as with 64-bit computers, it may also simply allow the device to run with fewer problems.

When I spoke to Donald and Geremy Mustard of Chair Entertainment, the company that makes Infinity Blade and that demonstrated Infinity Blade III on the iPhone 5s, they said the new phone’s 64 bitness gets the phone's other tasks (background, OS-level stuff) out of the way. They did note, however, that the iPhone 5S allowed them to flip on nearly all the visual special effects switches (reflections, fog and so on) in the Unreal engine, which drives the stunning imagery in Infinity Blade III.

While I also couldn’t test the new M7 coprocessor, an A7 companion piece of silicon that will read all the input from the built in accelerometer, gyroscope and compass, this could be one of the most important pieces of stealth technology in the phone. Apple introduced a CoreMotion API, which partners like Nike can use to build more comprehensive health and fitness apps.

Apple could use this chip to drive interaction with another device: the long-rumored iWatch. The only question is whether Apple will wait to gather more telemetry from the M7 before launching the iWatch this year, or hold off until 2014. In the meantime, there’s not much for typical consumers to see on the M7 front.

The iPhone 5S is very familiar. Its size and weight are exactly the same as the iPhone 5. It has the same retina screen. All the buttons (besides Home) look the same. The biggest difference for most users will be iOS 7. Its new look combined with this more powerful phone and some of the landmark features –- iSight camera, Touch ID –- should make the iPhone 5S feel less like an upgrade and more like a reboot.