The steripen is one of those products that people love or hate, very little middle ground! It either works or it doesn't, leaving very little room for moderately satisfied, especially considering the price tag. I've had no problems with mine, though I have always been cautious to prevent exposure of batteries to the cold. Seems as though most horror stories relate back to the batteries in one way or the other, but I'm no expert. Roger Caffin's BPL review is very helpful.
In any event, like you, I would be very reluctant to rely on the steripen, or any other single option, as my sole means of water treatment. I like the redundancy of aquamira for very little weight (haven't tried bleach), and it is waiting if the steripen konks out. On another hike, with different needs, I would probably leave the steripen behind altogether.
The issue of untreated water on cap threads is addressed in the comments section of Roger's article- proposed solutions include not worrying about it at all, wiping off the threads with a cloth, and loosening the cap and sending a little water through to flush the threads. Ultimately a personal decision.
A consistent theme in discussions of the steripen is that it requires a reworking of how you treat and drink water. For example, pump users can no longer suck water out of shallow or hard to reach places and must find some other way to get water into a container when submersion is not easy. Pump or chemical users may find that their old drinking containers have narrow openings and won't work with the steripen. Other questions arise. Treat in a wide-mouth hard or soft nalgene and assume that water circulates enough that the bottom gets treated? Treat in a more conveniently shaped container, shallower with a wider opening (cook pot, plastic bottle with the top cut off, heavy duty plastic bag, platypus with bottom cut off, etc.), that is then poured into a drinking bottle? In this case, where is that container stored while remaining easily accessible?
I haven't arrived at the perfect solution for myself yet.
The frontier pro would require a dedicated dirty bag such as a platypus- you already would have on with the AGG rig, I suppose. This would be filtered into either a drinking vessel, or some intermediate container, then steripenned. Granted, this full process might be a bit of a hassle, maybe too many moving parts, but I only anticipate using the frontier pro when sediment and/or taste is a big issue- most of the time a steripen by itself would be just fine.
Anyhow, I'm sure I'm missing something, and would love to hear ideas on how to make the system more convenient.