Intros (assuming 4 manips):
Blue wastes 7 frames per hard reset
Difference: Red saves 28 frames, this will never change.

Nido manip FFEF:
Red; ~597 wasted frames, 54/60 reliability incl yoloball frames (56/60 to get FFEF)
Blue; ~511 wasted frames, unknown yoloball frame reliability but 55/60 to get FFEF and the "base" yoloball frame is success.
Difference: 86 in favor of Blue (I do know this is the difference, the above numbers might be slightly off)
Chance for the situation to change: High in theory, but no-one is working on it right now. Current methods seem inefficient.

Yoloballable Paras at start of moon, no redbar:
Red: 0 wasted steps, 1 A press, 0 encounter chances, 58/60 reliability
Blue: TBD (not searched yet)
Chance for the situation to change: 0 A presses probably isn't happening, but one would imagine both games should be able to get 58/60 with 0 enc chances. The ideal would also be one Paras manip that gives YBF on both redbar and nonredbar, but that's less likely to be found easily.

Yoloballable Paras at start of moon, redbar:
Red: 0 wasted steps, 2 A presses, 2? encounter chances, 58/60 reliability
Blue: TBD (not searched yet)
Chance for the situation to change: See non-redbar above. Same situation.

Nerd to Killable Paras path (after fighting R3 lass)
Red: 0 wasted steps, 0 A presses, 3 encounter chances, 46/60 reliability with 17 & 18 clusters
Blue: search still in progress, but currently best is 0 wasted steps, 0 Apress, 8 enc chances, 46/60 with 17 cluster.
Difference: Advantage Red by ~2sec as it stands but Moon manips are still very much an "in progress" thing.
Chance for the situation to change: Mt Moon manip still has a long way to go. Watch this space.

Moon Lass to Catchable Paras path (after taking center)
Red: 2 wasted steps, 1 A press, 0? encounter chances, 53/60 reliability to get the Paras, and 52/53 yoloball frames. Unknown how much already having a Paras in your party influences this manip (or rather, its encounterless variant)
Blue: 2 wasted steps, 1 A press, 0 encounter chances. 54/60 reliability to get the Paras, but only 1/54 gets good yoloball frames.
Difference: Still a huge advantage to Red because of yoloball frames. Red wins beginner friendliness too because Blue path is from the program HTas, which generally produces zigzaggy paths.
Chance for the situation to change: Same as other Moon manips, very very high.

Trash Cans
Red: 1 wasted steps, 0 A presses, 53/60 reliability, 33 cluster
Blue: 0 wasted steps, 0 A presses, ??/60 reliability, ?? cluster
Difference: Advantage Blue by 17 frames provided the reliability isn't terrible.
Chance for the situation to change: Zero, search space for 0 extra step can manip has been exhausted.