In No Particular Order:
First,
It is unlikely that a Moderate Scenarios will result in nothing at all for the Aces to do, and regardless of that the Aces having nothing to do is far preferable to the non-Aces having nothing to do (Because the Aces have to babysit them). The Aces are already incredibly skilled and Shuri has fought in formations before, a single exercise of minimum effort is not a big deal. In addition, there are plenty of things the Aces can do during the exercise, in addition to serving as an emergency safety they can 'scale down' and practice lesser used skills (Spotting, speed, recce in force, whatever) or serve as evaluators for the team (Evaluating teamwork by the other members of the squad, figuring out advice for individual members, etc.) or dedicate themselves to being the equivalent of a High Yield Weapon (In a situation where you would normally call for a High Yield Weapon you instead yell 'Shuri' or 'Anna' or both and great things happen) or even handicap themselves and fight alongside the squad (One gun, no items, final destination!). We can seriously just declare that Anna is melee-only or one-gun-only or no-reloads for the scenario and declare something similar for Shuri. It is easier to scale Shuri and Anna down than it is to scale the Non-aces up.
Primarily because we can't scale the Non-Aces up.
Second,
A Moderate scenario is not a non-realistic scenario, nor is it a less-realistic scenario than a Difficult/Impossible.
These are all historical scenarios.
This happened in a real life situation. By definition. This is an actual use-case for Valkyries, by definition. The description even makes it sound like this is a more likely use case for Valkyries than the Difficult and Impossible scenarios which include 'everything is fucked', 'this one-off scenario that's unlikely to be replicated', and 'everything is fucked again'. Red Tide is an Assault-Prep scenario, the sort of thing we're almost certainly to be deployed for at least once, Single Sweep is a combat sweep, the sort of thing we're almost certainly going to be deployed for at least once, Blitzkrieg is Search and Destroy. The Moderates are all scenarios that seem relatively common in an actual battlefield. We don't have real reason to expect them to be non-realistic or non-representative. We should do Difficult or Impossible scenarios in the future, but this is Day Four and I don't see any reason why we need to do it as our first team exercise.
Third,
A safe environment for co-operation to grow fits Moderate very well. Red Tide and Single Sweep seem to fit the description more than literally any Difficult/Impossible scenario, and I'm assuming that the Randgens are at similar difficulty levels to the historical and future scenarios.
Koujirou's intent should be ignored since he's a harem MC and an idiot. He is by no means even a layman when it comes to figuring out team building exercises.
We're both nominally understrength flights, being the strongest flight in the year gives its own advantages for stuff like the competitions and placements, a concentrated 'high performance' flight made of everyone who's dedicated to holding top ranks will likely encourage higher performance from each other, etc.
There are loads of reasons to merge the flights besides anime logic. I could probably grab one of my psych textbooks and grab some stuff on high-performing teams from there over the weekend, if you want.