Personally I don't mind the lack of infected kicking around, I think it makes sense. If you've got a gun and some know-how (which most of the people who have lasted this long probably do) they're not a huge threat unless you get taken unawares and/or overwhelmed by a big group, both of which are unlikely outside of bigger towns and cities. I think it's reasonable that they're a constant threat in the backdrop, as opposed to being the main challenge. Narratively, you limit yourself enormously if your protagonists spend a lot of time tackling an antagonist whose motivations are obvious from the start and are incapable of changing.
I haven't played through the games, but my suspicion is that achieving immunity to the fungus wouldn't actually make much difference. The world would be still be fecked, pre-fungus supply chains and infrastructure would still be largely unfeasible because of population loss and the breakdown of political and social structures. I doubt a fungus vaccine suddenly means all the fascistic police states and bands of marauders settle down and beat their M-16s into ploughshares.