The side ops are technically never-ending since they reactivate after a while, so I don't think anyone should burn themselves out trying do them all (aside from the plot-related ones for the Paz subplot, Man on Fire, AI Pod, etc).
They're mainly a way to ensure that 1) you always have a prisoner to rescue, a soldier to extract, a tank unit to defeat, etc, should you want an objective while free-roaming in the sandbox, and 2) to provide another way to procure resources without having to repeat story missions (although you can still replay main ops if you want).
I'm thankful for them. Sometimes I'll clear out a few side ops in hopes of a new prisoner extraction mission appearing.
I think Kojima himself at one point stated that side ops are meant to be content always available in order to have small bursts of MGS dose long after you have completed the game and just want to get your fix.
They are certainly designed as such and its great to have them post campaign in order to just go out and try out all kinds of crazy things.