Since melee 2.9, specifically when fighting the Profit Taker, I can no longer melee at all (eg. with Scoliac) when equipped with an Arch-Gun (e.g. Corvus). I'm forced to un-equip ithe Arch-Gun t if I need to use melee attack (which I do by going into Arch-Wing mode, then back out, which causes the Arch-Gun cooldown).
From Orb Vallis, if I am using my secondary weapon (eg: Catchmoon kitgun), then switch to Arch-Wing, and then exit Arch-Wing, the game doesn't remember that my last used weapon was my secondary, and instead automatically switches me to the primary weapon if I use LMB. At present, I can only consistently get to my secondary by unequipping my primary weapon before starting the mission.