I think I only found 4-5 places tops in the campaign where placing checkpoints wouldn't really have much of an impact on mission flow. Let me look at my "upgrade" spreadsheet...
OK, here's my list:
-The Kinney mission (Nipheleim 2): right after the destruction fo the Kinney and the first wave, makes you skip over the "fly towards the doomed battlegroup" part straight to the first real challenge of the mission.
-Hyperion 1: right after jumping in, basically skipping the jump sequence. Or possibly after clearing the jump point, before the battlegroup starts warping in.
-I also wrote in Freya 2, after saving or failing to save the Cabot, before the mission's final sequence, but after rethinking about it, the mission's pretty much over at this point anyway, so scratch that one.
-Right before engaging the Wratghar in the final mission: the action before that doesn't affect the rest of the mission and merely serve as a prelude to the big fight, while still taking about 5 unchallenging minutes.
So 3 checkpoints mostly aimed at taking the player straight to the action, out of 50 missions. I'd have to restudy some of the more "marathon" type missions, I'm sure a couple more could be squeezed here and there.
What's funny is that WCS's mission structure is perfect for including checkpoints, thanks to the fact that you have invincible wingmen and the mission division in navpoints.
Compare to Blue Planet 2 (from what I can recall right now), which introduced the checkpoint feature:
-one or two in the cost of war, the first mission of act 1, a lengthy but chatty escort mission, with a rather slow pace, the big factors being the state of the ships you are defending.
-in the first mission of act 2, after your first try, you get the option to skip the dialogue tree, conserving your previous choices.
-one in the middle of aristeia, after fending off the inital attack against the two frigates and logistics ship, the big factors being how much damage your ship has taken (especially if you decided to fly a GTVA fighter), how much damage the Indus has taken and whether or not the AWACS was destroyed. It's a rather lengthy, action-heavy mission, in which the first part has a moderate influence on how the second part goes.
-one in the penultimate mission, after having succesfully disabled and disarmed the Alliance corvette. It's a short mission, with two distinct bursts of action, first dealing with corvette's escort, then the cruiser's. The checkpoint is there mostly because disabling the corvette is a rather tedious and low-challenge task.
-two in the final mission (Delenda Est), a lengthy, action heavy mission in which you barely have time to catch your breath between waves. The first checkpoint is placed right after the last bombers/capships threatening your initial strike force are down, as backup arrives to spearhead the assault afterwards. The second checkpoint has been placed before bombers start attacking your initial strike force again.
Checkpoints are completely absent from act 3.
So basically 5 missions out of 15 (only counting act 1 & 2 or cutscenes), with two not featuring any action. Their use of checkpoint is interesting, in 3 cases, they're here mostly to prevent player boredom over multiple attempts, but in two cases, they're in the middle of extremely action-heavy missions, particularly Delenda Est. Here, the checkpoints are arguably responsible for allowing the mission designer to make the mission harder than usual while limiting player fatigue on their inital playthrough (checkpoints can't be used while playing from the techroom).
Again, keep in mind that these are 2 vastly different projects in terms of gameplay, storytelling, history & development model.