(1) Scan document at very high resolution as a JPG and then use a third-party program (like Photoshop or whatever) to re-encode the JPG at your preferred low resolution.
(2) Scan document at your preferred low resolution as a JPG straight away. Don't re-encode afterward.
Intuition says that the results of #1 vs #2 should be identical, or that #1 should be worse because you're doing two passes on source material. But I always get better results with case #1 (i.e., high-res scan and re-encoding afterward) regardless of the type or model of scanner, or whether the scanner does the JPG encoding on-board the device itself or through a Windows/Linux/Mac driver bundled with the scanner.
My theory is that scanner manufacturers are deliberately choosing the JPG encoding profile that gets them the fastest result. They want to brag about pages per minute which is an easily measured metric. Quality of JPG encoding and file size take effort to compare, but everyone understands pages per minute.
If anyone has contrary experience I'd like to hear it. I've been seeing this for years with different document scanners and flatbed scanners -- regardless of how I tweak the scanner's settings, I can always get good quality in a small file by re-encoding afterward.