Conceptually, I think of the mechs as 'real'. So if I have one mech with my Longarms loaded, I can't have those same weapons mounted on another chasis just because it's on another 'team'. With the restrictions that each mech can only be assigned to one team at a time and each weapon can only be assigned to one mech at a time, having multiple bays would be awesome.
Teams could be more abstracted that bays - just a particular selection of mechs for particular tasks. One big bay with all your mechs in it, but you can only field 5 at a time in pre-defined groups.
While we're at it... I suspect the devs could make some money with customizable bays. Sell cosmetic upgrades - different exteriors visible, maybe the player's major awards as banners on walls or hanging from the ceiling, stuff like that. Going back to the 'teams' idea - that could be a purchased upgrade too.