I don't mind the endings for the main story being a bit linear and having resolutions that make sense its more for all the side stuff and whether certain settlements thrived or died. My ideal answer would be to have sequels take place in new settings and have the occasional nod or snippet of information about what happened in the last game. You could even have contradictory takes on the events of the game showing just how large the legend of the protagonist has become.Fallout 2 straight up canonized tons of Fallout 1 with the journal of the Vault Dweller. It acknowledged no choices you made, and part of the reason is that there weren't as many big choices in Fallout 1 as people think there are. The other part is that it didn't even import saves from 1. Canonizing certain aspects of Fallout 3 would be pretty easy. It's already canon that Megaton wasn't blown up and that the Lone Wanderer helped the BoS nuke the Enclave.
This would be one of those things that old fans would look like faggots for complaining about. Just like when they talk about ending linearity when Fallout 2 has just as linear an ending as 3.
Say you have some characters taking around a fire about the defense of Big Town and how the legendary Lone Wanderer was there and taught the residents how to shoot guns before another cuts them off and tells them they were wrong and they actually saved the town by fixing the scrapped robots there. The third character around the campfire just chimes in and says they heard that the Lone Wanderer just took a super sledge to the attacking mutants.