So then how would YOU design combat encounters to work against having just those 3 classes shine? How would YOU envision a system where Rangers and Thaums aren't > all?

Personally I think the first step would be to "fix" Emulate so that Thaums can't solo NMs. There's no reason any one class should be able to solo content that others need groups for.

As far as Archers go, give directional AoEs (not necessarily front or wide) that extend past an Archer's range. That way they're in just as much danger as everyone else is. Their ability to stay out of AoE range is a great asset and if you can take that away there will be need for others. Other players who are closer to the enemy can more easily get out of a cone AoE's range by moving around it. Archers are further away and thus must move a greater distance to get out of the cone. Even further maybe give enemies attacks lie Arrow Helix and Iron Tempest that actually don't hit melee range but have a huge radius.

Aside from that giving enemies the ability to reposition themselves mid-fight would help at the very least keep all classes on their toes. What was once at max range could in seconds be in your face.

Outside of things like that though I'm not sure what you could do about fixing it aside from straight numbers balancing.