I've been using a Steripen for years. At first, I had all the same concerns listed here, and thought long and hard about the fact that the water was not "treated" in such a way that you could "rinse" the cap threads or easily refill the bottle without either dunking it or carrying a second filler container. But here are my impressions...
Batteries: The steripen I have is just the regular classic version. Batteries last FOREVER once you switch to lithium ion like recommended, but never the less I change them every season. The LED signals when they are getting low, but I've had them get low.
Malfunction: At first there were a few times I thought mine was not always turning on or working correctly, so I went back and re-read the instructions very carefully. The LED tells you everything you need to know, and I realized the most of the time what I thought was a malfunction was just me putting the lamp in too early, if you wait another 2-3 seconds for the LED to start blinking (which signals it is now ready to immerse into water) and then begin, it works perfect. At the end of the treatment, the LED also tells you if everything went correctly.
Cross Contamination: Carrying a second "filler" container is not necessary in most cases, and I've never done it once, though I was fairly careful not to contaminate the threads too much. A few years ago they came out with a Fits All Filter, which makes things much easier to just dunk the container (I still dont dunk the lid, as its easy to keep it out of the water). Somewhere buried in those instructions Steripen actually states something to the effect of "the small amount of untreated water left on the cap threads is negligible and not enough to contaminate yourself." BOOM! Once steripen reached that conclusion and actually put it in writing, I was convinced they must have put the effort in prove it statistically true under normal circumstances, and I stopped worrying about the damn threads. It is quite significant for Steripen to actually state such a fact in writing, and it shows they not only acknowledge the potential, but appear to be comfortable enough to state it is not a problem. I would also ask the question to filter users, do you really actually store all the dirty side tubing and intake float thing in a separate container than the clean side filter components, between uses??? This is a similar situation.
Lastly: I have never been sick, and that includes a few trips to the dreaded chicago basin. While it has been correctly pointed out that is not proof of anything, I will say that if I were to pick a location that was likely to have abundent Giardia, that would be one (assuming all the goats and deer are crapping in the stream in close proximity to the peoples camps on a daily basis). And as far as crypto, just read CO Native's story and you think twice about methods that dont kill that rare virus. Good thing my Steripen has that covered, and without a 4 hour wait.
And just for the record, I often bite through my wet fishing line when changing a fly, lick the dirt off my camel back bite valve after I set my pack down in the dirt, spit river water out of my mouth after being sprayed from a rapid, and brush my teeth with faucet water in foreign countries but spit it out after words, chew my fingernails teeming with bacteria, etc. The point is, your getting nasties in your mouth all day long no matter what you do. It's a question of there being enough volume to reproduce, which boils down to statistics. At some point you need to stop worrying about water and start worrying about being hit by lighting instead.
I do like the idea of chemically treated water for simplicity and less weight in the pack, but I'll carry the extra couple ounces to save 4 hours of waiting or a 6 week round of crypto. I still use my filter, but not for the clear water in Colorado.
Edit: Here is a link at their website regarding their stance on the untreated drinking surface, refer to #5. http://www.steripen.com/steripen-misconceptions/