Personally, I think you're falling into the old habits of trying to conserve as much battery power as you can, and over-reacting a little. Don't exchange the phone, it sounds like it's working correctly. You also have plenty of battery power in this phone, just enjoy it! Here are some direct answers to your questions though.
No, there is no setting I have seen to make active notifications only flash once. The phone will continue to "breath" at you whenever there are non-dismissed notifications. From the video's I've seen on the moto x, and the behavior of my phone over the past month, I believe your understanding is incorrect. The phone continues to breath until you dismiss the notification. As far as being in your pocket, I'm fairly certain that the notifications stop when the proximity detector is triggered. You
might be able to test this by placing a small piece of paper on the upper left hand corner of the phone and seeing if it stops. I haven't tried this test, but I will. One thing that would be educational for you is to watch some of the promotional videos on the development of the Moto X (basically the same hardware and software of our phone). Motorola put a lot of effort into programming that knows when you're around your phone, and having it "breath" when it knows you're near it. I've played with this feature myself by having the phone (with no notifications waiting) on my coffee table (soild wood), and tapping the table almost 3 feet away, and the phone would wake up, and breath the time at me. I actually think Motorola did an awesome job with active notifications, and I feel it works very well. I think they used the combination of sensing vibration, movement, and proximity detection in order to do it, and it works great.
Now, with all that said, if active notifications isn't for you, you can simply turn it off. You can also set which apps trigger active notifications so that it only breaths at you when you really want it to. For example, missed calls, text messages, but not emails. I would suggest visiting this page:
DROID MAXX by Motorola Support | Verizon Wireless
Click on
personalization, then click on
customizing active notifications, and that will walk you through setting what apps you want to be notified with. I'll keep an eye on the thread if you have more questions, but I think your best bet is to just forget how you had to live with your galaxy nexus, and enjoy 3500 mah of battery power! Honestly, with the info you put forth here, I think if you return the phone, expecting something different, you'll be disappointed...