Simple answer to all your question and complaint parts: Consoles
You can now start to hate and detest: Consoles
The low memory on consoles is the prime reason for checkpoint saves that don't save shit. Did you never wonder why so many games for consoles don't remember what tree you destroyed, or what non-scripted building or vehicle you left destroyed where? It's because of console memory limitations.
And before you say, "but skyrim" .. yes, Skyrim manages to do it, but Farcry 3 is simply a port from consoles where the developer didn't bother to put in a proper save system not even for the consoles. So you can also blame laziness on developer part.