the idea is to give players more incentive to join factions, not to remove indy traders/smugglers/civilians/freelancers/etc. entirely.
We need more faction tagged/id'd traders. Factions like ALG, Kruger, BMM, Samura, etc. are all pretty much non existent right now. Why restrict yourself to a specific area when you can be 'generic' and go anywhere or do anything?
It is a problem IMO.
Personally, i think RP rules should be put in to make it so certain trade factions can only trade certain goods. Synth would be the only faction capable of transporting food rations, Ageira/Kishiro would be the only factions capable of transporting optical chips and gate/lane parts.
Civilian (i.e. "generic") traders would be relegated to low-profit items, and not be able to trade the company-specific products that make big bucks.