When using non-rogue squadrons, do you plan to have an order for everything all of the time (or at least when you need it)?
I like squadrons and when building a list, I'll usually assign squadron groups to a ship, where the size of the group is limited by the number of squadron activations that a given ship can support.
E.g. an AF2(B) with an Expanded Hanger Bay can activate 4 squadrons with a single order, so I will have it control a group of 4 squadrons.
Do you need to have this limit?
I think the question is more relevant for "support" squadrons - like a HWK that has Intel. This squadron is there to allow my other squadrons to move freely. With the example above, I could have my AF2(B) controlling 4 y-wings and simply have the HWK tagging along.
This won't diminish the effect of Intel as I can still order my y-wings when I need to, and the HWK can follow up by itself in the squadron phase.
It's a riskier way to work though as my HWK could be shot down before it gets to catch up with the rest of it's group, or my y-wings could be caught out of position without the HWK. But it does allow you to maximise the damage potential from your squadron order.
Another example I was considering was Yavaris (and Ray - of course) controlling 3x B-Wings with a YT-1300 a HWK as "uncontrolled" support squadrons.