I like the concept, Kitsune. I agree that hit locations are what make Mechs, and other BT units, different from a lot of other wargames. A friend and I went so far as doing damage/5 for the output, with some weapons needing to act like bays in DropShips in order to do damage at all, or have some sort of damage of 0 still causes a check on crits or pilot damage. This was modded off MW:Dark Age, though.
I'll point out the SilCore system behind Heavy Gear, Jovian Chronicles and other Dream Pod 9 games. You're still stuck with a single life bar. Now, while Heavy Gear does have a hit table system to account for what the damage does, you're only marking off one, maybe two boxes on the life meter.
This is one direction I would have wanted for Alpha Strike, a chance that something will still cause a crit (through location loss not tracked on the life bar), until you get to the auto crits from internal damage.
Maybe come up with a damage threshold value based on general location compositions. If your attack did this much, roll for crit. Maybe go so far as to apply that to the different crit results.
RE: Alpha Strike Crits - You're still rolling for a random effect there. Now, you're just putting some armor in front of them, instead of a life meter overall. Might as well be locations, then. Since you're making a single attack roll per unit, I don't see how the extra step of rolling for a location would add all that much to game play time. Unless you're doing Yu-Gi-Oh speed duels, and really plan on only taking, what, an hour(?).
You can come up with a simple diagram that lists in each location what will be lost when it takes internal damage. You wouldn't have to get complicated like with BT proper, just have that all effects listed are lost when internal damage happens. Not as strong as in BT, but it's still up there and would still feel like BattleTech as I view it.
Aside: On the flip side, a single life meter for a Tank's internals on a small card was something I've been looking for in BT. Call it structural integrity if you want, I've always found the different internal damage tracks for tank internals in BT proper to be baffling, especially when there's no damage transfer and that tanks are generally open on the interior, anyway.