That's how it is for most games. That's why you "play another game."
Well, my point now would be there should be more content or replay-ability to use those maxed out abilities and weapons. I guess I would consider a replay if I could retain my earnings, with the 2nd time through more focused on just having fun (please don't tell me there is an option for that).
I hate to keep referring to GTA, but at least you could amuse yourself, story or not, with free roaming using your skills with your imagination or get a wanted level. Basically cause trouble, whereas after the story in Farcry,, there are only civilians who you are politely reminded you can't kill. Oh, and animals, but that's pointless and mundane when you have nothing to craft.
I'm on my second playthrough now, and now that I know how the story goes, I am focusing more on exploration and crafting. I've barely got into the story on this playthrough, I've just been liberating camps and towers, and crafting stuff. The game is quite forgiving, actually, in terms of not forcing you to do the story missions when you don't want to.
I just did the first mission with Daisy and the doctor, and I've liberated nearly all the towers and outposts on the northern islands. It's great having so many free weapons so early in the game.
I wish this game had a better save system, though. I don't like it how it allows you three slots, for different games, and you can't overwrite slots, or save to a new slot. I like being able to replay missions, from different stages of the game, when I want to.