IF you were not hunting in the water, and easy on your equipment, I would DEFINITELY have said the one with the carbon-fiber shaft upgrade. BUT -- if you plan to go in the water, that changes the equation; in that case, I'd go with the one with warranty.
Coil ear breakage can be made "rare," if you keep an eye on your washers (change them if they wear), and similarly, don't over-tighten your coil bolt (if the coil ears bend inward substantially when tightening the bolt, it's time for new washers). And IF the ears do happen to break, they can be repaired inexpensively. Meanwhile, if you opted for a new coil, it's still only a couple hundred dollars (though not sure if the new coil would include a new warranty, and if so, for how long). Anyway, from that view, not having a warranty on an Equinox would thus not bother me; in fact, my own units are out of warranty and I don't worry about that at all. Further, regarding shafts, the stock shaft leaves alot to be desired in my opinion, so a carbon-fiber shaft is a very nice addition. BUT -- I don't take my machine in the water. If I did, I'd be purchasing an additional Equinox, WITH warranty, and would ONLY use the one with warranty in the water.
For comparison's sake, I believe a new control pod (if your control pod had to be replaced by Minelab outside of the warranty) runs $350 (though I will note that I have also heard that you can get a "refurbished" one for $225, but not sure what a "refurbished" one would entail). Also, for that $350, the new unit would be under a new 3-year warranty, I believe. Meanwhile, as noted, a new coil runs about $250, and a carbon-fiber shaft runs about $150. So hopefully that helps you to "value" your decision properly.
Again, coil ears CAN be repaired, but a drowned machine can't...so I'd say if you plan to use it in the water, unless you put $350 aside "just in case," I'd go with the warrantied unit and then save my pennies for a shaft upgrade, if it were me.
Hope that helps!
Steve