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I love the Raspberry Pi as a computing platform but sometimes I cannot stand the sluggish performance of the device. Occasionally when I'm browsing the internet or even trying to open the regular applications menu of Ubuntu Mate, some programs won't respond. After observing the CPU usage during these moments of lag, I can determine that it's not the CPU that is causing these problems. Before and after overclocking, no core hits 100%. Is it the memory lagging the system? Or is it the storage? My first guess is that the main bottleneck of the system is the microSD card. Would using a bootloader on a microSD card to boot an OS off an external hard drive/SSD benefit the performance of my system?

I already boot off of a UHS-3 microSD card.

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    This is simply the nature of computers in general. As in, CS 101. Transfers within the CPU are faster than transfers involving RAM which are faster than transfers involving persistent storage. Period. The same situation everywhere. Reality, not fantasy. If everything you did just cranked the CPU to 100% and involved no I/O bottleneck, then something weird would be going on. As with your laptop/desktop/whatever, you can add any hardware you want -- the CPU will always be many orders of magnitude faster. It only runs 100% when little or no I/O is involved. – goldilocks♦ Oct 5 '15 at 21:51
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EDIT: A little unrelated, to the central question, but applicable to the core concern, I found this link which explains in detail the issues with using flash memory. Odds are it's the flash memory that's bogging you down.

ORIGINAL: I can't find the link I had for this, but in theory, yes. SD cards were not really designed for use like this, nor were USB. But of the two, USB are generally faster. Though there are some cases where it might not be (a cheap USB 1.0 vs. a really nice SD for example).

For these reasons, many people have set their pi up to have the file system on a usb stick, like you had mentioned. Though that is not a usb hard drive, it's still to the same effect.

In my experience, though, having the file system on a USB did not really make any noticeable difference. Mine in just one case, but I think it would be unfair to not mention that. And if you're trying to cease the lagging, this may make a dent, but probably won't finish the job.

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