As far as the simple answer to why so much more for big healeys, the simple answer is how much somebody is willing to pay, so how come somebodies are willing to pay a lot more for Big Healeys?
Please understand this is being written by a guy who has owned and loved both.
Yes from a practical standpoint the Healey is not that much if any better of a car, smaller trunk, as mentioned ground clearance and cockpit heat problems the TR6 doesn't have, but if people bought collector cars from practical reasons we would be lusting after 20 year old Tauruses and Corollas (an aside: Blech!!!)
One reason is simple supply, a lot of TR6s were bought and preserved as second cars, collector cars, etc. there are many more nice restored and original examples around.
Styling is a matter of taste, and some like this and some that, but the healey is nevertheless a relic and reminder of the days when the Brit sportscar was at the top of the world for value and still trendsetters in many ways, when the big healey shape come out there were square rigged T series MGs, and Morgans and such, The handsome but slab sided Jag XKs and triumph TRs. The Healey was the prettiest most stylish thing to come out of england until the e-type, with the possible exception of the much more limited production AC Ace. It also compared pretty well with the best the Italians had to offer.
The TR6 is a very handsome car as well, but the cars of the 70s with their federally refulated rubber protrusions and lights are generally viewed as somewhat compromised from a pure style stanpoint.
The Healey, though similar to the TR 6 in performance, was higher in specification (US Spec.) at 100 horses and change for the TR vs, a buck fifty for the last Healeys, and the Healey offered it sooner.
Lastly and I think most important is the era they represent just as sixties muscle cars command more money for their chrome, lack of emissions controls and reflection of an era when cars were unfettered with emmissions and safety regulated design, so the 50s and 60s british sports cars will bring more money than the 70s items, the Brits did not react to emissions and safety regs well (The TR6 better than most, esp. compare and contrast to the rubber bumper single carb MGB), the Germans and Japanese did a much better job of this and pretty much wiped the British off the import car map by the end of the 70s (they had in fact pretty much killed the sedans and compacts by the end of the 60s with the exception of jags and rolls royce and such).
The 60s reflect the last days of the British sports car at its Zenith, and the 70s represent the British Sports car in decline, the prices reflect the era the cars were produced in.
That all being said I sold my BN1 Healey 100 to buy and restore a TR250, I could write a long story about that decision as well .....
O yeah and cars named after and percieved to be built to the vision of one man seem to do better in the collector car world, Ferrari, Bugatti, Shelby Cobra
edited for spelling, proably still missed some.