My humble thoughts are that a decision of this magnitude deserves some honest reflection on what the owner wishes to do with the car - what is he or she looking to accomplish by owning the car - factors beyond merely what the car 'might' be worth to the next person to buy it afterwards. If the car will rarely be driven, and is purchased mainly for its appreciation value, it would be hard to go wrong with either choice - both are considered "Blue Chip" collectibles. In fact, the Gullwing variant of the 300SL was called the "sports car of the 20th Century" by a jury of trade journalists. It's highly doubtful either car will depreciate much, if at all. If the car was used for track events, the choice is pretty clear, the rip-snorting Cobra has the requisite sights, sounds, and stripes. (Although the 300SL was also based on a very successful race platform that won LeMans outright in the 1950s). On the other hand, if the car is intended for touring on the open road, especially with a Significant Other - the choice is also clear - the 300SL with its roll up windows, hard top / soft top choices, more comfortable seats, better storage space, etc. And with the 300SL, bystanders and others would never mistake or assume a real one for a clone or replica, unlike with Cobras, unfortunately. Finally, regarding documentation, not only is Mercedes-Benz factory support still very strong for the 300SL series, (unlike Ford for the Cobras), there are also several strong, close-knit 300SL support groups as well (GullwingGroup.org for one). Even the factory (the Mercedes-Benz Classic Center - located in California) can directly document, restore, consult on, or just service 300SLs.
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