For me, Traveller is the 3I. All my Traveller campaigns take place in the (mostly) canon 3I, using the MegaTraveller timeline, but Virus never hits. All my campaigns have taken place in the same 3I, with the actions of one campaign being referenced in others.
Ruleset is according to the type of campaign me and my players want.
For campaigns with lots of crunch - military, trade and commerce, mercenary - we'll use EABA. It's a very good drop-in replacement for the Traveller rules.
For other, less crunchy campaigns (especially those focused on characters, families, and their interactions), I run using Fate Core, with addendums from the various Fate toolkits.