Effectively it sounds like a chaser pattern but done as quickly as possible for persistent vision.
This appears to depend on how limited you are on bandwidth, and your bus protocol. 50hz x 24 bits x 2 LEDs (as you said you can drive 2 at a time) equals 2400 bits per second. I wonder if you can easily double the data rate to 4800 bits per second, so you don't sacrifice bit depth for a higher refresh rate.
Do you think letting the user choose between high refresh frequency and colour variety could help? So you could choose between 50Hz & 24-bit, 75Hz & 18-bit and 100Hz & 12-bit colour?
This appears to depend on how limited you are on bandwidth, and your bus protocol. 50hz x 24 bits x 2 LEDs (as you said you can drive 2 at a time) equals 2400 bits per second. I wonder if you can easily double the data rate to 4800 bits per second, so you don't sacrifice bit depth for a higher refresh rate.
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