I look at the Jet series as a kind of "premium" version of the Fenix lights, especially in terms of the beam. Fit and finish issues aside, the Jet's beam wins, hands down (No donut hole at ANY focal distance). IMHO, the design and finish are superior as well (not counting the apparent tritium debacle that some folks have had to deal with).
Keep in mind that the Jetbeam project is 'semi-custom' compared to the Fenix mass-produced armada.
Back to the original question (will 2 stage Jet kill Fenix?), I'd say definately not. The Fenix lights are readily available, and are of very good quality for the price. The Jets are significantly more expensive for what some might not even consider much of an upgrade and are pretty much only available from one seller. For the same money, you can get a Fenix L1T and already have a halfway-decent 2 stage ability and the same battery flexibility as the Jet.
Additionally, this legendary 2-stage switch has apparently been very difficult to produce to Emilion's satisfaction and has been delayed several months passed it's original projected release date. As it is only to be produced in HA-Nat (meaning a mismatch unit for those that plan to use it with the newer black lights) and is really just a follow-through of a promise and not a for-profit accessory, I very much doubt the run will be very large. There are only so many original HA-Nat AA Jet-I owners out there, and of those, only a (large) subset will be buying. Many folks may just opt to suck it up and order the MK-II, which is almost twice the cost that you can find a Fenix L1P (and the old original 2 stage Fenix mod still seems to be holding up pretty well).
I really like my Jet-I and am anxiously awaiting the 2 stage switch for it. However, that doesn't mean I'm glad I didn't just wait for a better product (MK-II) to come out. I very much hope that I will be satisfied with the 2 stage switch, because my wallet won't be happy with dumping another almost $70 on a light- those days are coming to an end until the next great generation of LEDs changes everything.