CPU: It really doesn't matter. The OS / apps have to run smoothly and supposedly they do on the Pre3 (and Pre2). Even the "fastest" Android phones stutter.
RAM: 512MB is enough. There's no need to add more, it would only make the phone more expensive.
Fingerprint: Nice, but this is more of a gimmick than an actual mainstream useful feature, at least in my eyes.
Storage: I personally wish the Pres/Pixis would be expandable with microSD cards, but I think 8 or 16 GB is enough, unless you're carrying around several HD movies. Again it would also make it more expensive.
Resolution: Doesn't really matter. DPI is more important. I think the recognizable difference between the Pre3 screen and the Atrix screen is negligible (not taking screen technology into account). Also screen size is a matter of personal preference. For me ~3.5" is the sweet spot.
Battery: we'll see what the real life performance of the Pre3's battery will be. No need to hate it already. Again mAh is just a number, it matters how efficiently the OS handles power consumption.
1080p recording: Nice, but not everyone needs that. Adds costs.
3D: see Fingerprint
Camera: Megapixel is only a number and says nothing about the picture quality. Surely the Pre3 camera will not be the best, but it will suffice. Again it would add costs. People who need (for whatever reason) a high MP camera in their smartphone may look elsewhere, it's good to have choices
iPhone 5: we know nothing about iPhone 5, no need to speculate.
In conclusion: I don't think the Pre3 is already outdated. It is also cheaper than the phones you mentioned. Sure, these are phones that are superior in some spec, but unfortunately one just can't have everything. Also, the Pre3 is marketed more towards the business user, so I guess HP felt no need to add 12MP cam, 3D and 1080p recording. But don't get me wrong, all those features are nice to have, but all those things you mentioned do not automatically make a good smartphone.