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I don't see why it wouldn't; give it a shot! Worst case you can re-install Sierra through the recovery partition.
 
Well, it worked - Mavericks caused a kernel panic, and El Capitan worked great. Installed El Capitan onto an old USB 3 drive, and it was slow...

I plan on leaving Sierra installed on this laptop, and would like to run El Capitan from an external drive. In this scenario, what would be faster - a USB 3 Flash Drive or a Thunderbolt SSD Drive?
 
An SSD is always faster than a flash drive, as well.
Hmm

I ordered a very fast 64GB USB 3 stick to try.

Is there an external SSD using Thunderbolt that's recommended?
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I am curious, why do you want El Capitan and not Sierra?
There is an app I need to run - works in El Capitan and has been deprecated for Sierra. I'm fine leaving Sierra on the laptop, and running El Capitan on an external drive for occasional use.
 
My new (purchased 2 weeks ago) 2015 MacBook Pro 13" came with El Capitan pre-installed.

Runs fine.

Not interested in Sierra yet.
 
Hmm

I ordered a very fast 64GB USB 3 stick to try.

Is there an external SSD using Thunderbolt that's recommended?

There are very few USB 3.1 Gen 2 hard drives and even fewer Thunderbolt 3 drives, here's my short list with comments:

  • LaCie 2TB Bolt3 $1999 [this will be the ultimate Thunderbolt 3 drive, two SSDs striped; 2800Mbs throughput]
  • SandDisk 1.9TB Extreme 900 $750 [this is the only USB 3.1 Gen 2 interfaced external SSD]
  • Samsung 1TB T3 $350 [if you want Samsung and you can't wait for their SSD announcements at CES, particularly an update to the T3 external SSD — the current one is USB 3.1 Gen 1, unfortunately]
  • Seagate 8TB Innov8 $320 [the biggest USB-C USB 3.1 Gen 2 drive out there, NO POWER BRICK]
  • CalDigit 2TB Tuff $179 [this is a regular hard drive but it's one of the few with a USB 3.1 Gen 2 interface]

As you can see, the list is incredibly short. Most manufacturers have yet to convert their lines to USB 3.1 Gen 2. And the situation is even worse on the Thunderbolt 3 side, where you can count drives and enclosures with one hand.
 
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To bring conclusion to this thread, and to help out others who may be in similar situations...

The old USB 3 drive I tested everything out on was a 32GB Corsair Flash Voyager Slider (USB 3.0) and it was painstakingly slow. I ordered a 64GB SanDisk Extreme CZ80 (USB 3.0) and it was lightning fast! Incredibly fast!

Straightforward and easy process: Formatted the SanDisk for a Mac, mounted it with a partition table, downloaded and installed El Capitan to it, and it worked great. And while I haven't run any benchmarks, booting and running programs off this SanDisk feels nearly as fast as the internal SSD in the MBP.

Had the SanDisk been too slow, I was prepared to purchase an external SSD over Thunderbolt, but this works out much better. The SanDisk is very portable, and 64GB was more than enough. And now I can boot El Capitan the few times I'll need it, and continue running Sierra 99% of the time on my MBP.
 
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