Side Ops that are plot important are coloured yellow, and a few of those important side ops lead directly into main missions.
However, the way the game is designed (I.e. a big grind), you're pretty much expected to at least do some of the optional side ops. You have to play through some during the second half of the game to unlock missions, like how Peace Walker's final chapter worked with the 'do a few side ops, do a Zadornov search mission' structure.
I'd recommend taking your time through it though, because even with just going through the story it's a stupidly long game, so it's not like you're gonna be able to blow through it over a weekend.