As complicated as their mission is, their goals are relatively straightforward, so viewers don’t have to try and figure out the rules of S.H.I.E.L.D. time travel week in and week out.
There’s more time for character development (and LMD Coulson nerding out over witnessing history) without — to quote Doctor Who — any “timey wimey” confusion.
S.H.I.E.L.D. has a goal: stop the Chronicoms from taking over the Earth by following their course through history on “tides.”
They can’t use the Zephyr as the kind of time machine that lets them jump back and forward however they want.