I thought the story was much better in FC1 than 2, not voiced all that well in some respects, but better story. Most of those whom didn't like it just couldn't accept the sci fi elements, and with many, it seemed like it was more an extension of their loathing fighting the Trigens than the actual story itself.
FC 1 also had better combat and story balance. It wasn't a failed RPG meets FPS sandbox attempt like FC2, where buddy assist missions were over before you got there, convoys circled endlessly until you destroyed them, gliders were ill placed, and the villain talks the protagonist into suicide with his political mumbo jumbo.
That said, despite respawning AI at checkpoints being annoying if you attempted to casually drive through them in broad daylight, there were several ways to deal with it that actually broke up the gameplay and made it less monotonous.
To deal with checkpoints I resorted to buses, boats, driving through quickly at night with headlights off, or carefully circumnavigating them while crouched, and I rarely had any difficulty doing it. Now and then I'd even grab a mortar canon equipped vehicle and blast from a distance before driving through.
As far as whether they're proper sequels to FC, Ubi has obviously taken liberties with only offering a vague theme similarity, vs continuing the actual FC1 story. I think that decision was largely to distance themselves from CryTek's sci fi oriented theme though, which many didn't like. They wanted to glom off their success, while omitting elements that offended many. The only way to do it was to change the story entirely. IMO, they could have picked a MUCH better story than FC2 had though.