Why? That's not really something I've heard before.
What I mean here has been well explained by Scidave. It's a bit stupid to just have to enter a level, grab some ressources, and exit the level by where we just arrived. And it's possible to do that at the very beginning of the game, because even the first levels have some ressources at their entrance. But rearrange the level design would not solve the problem.
Perhaps you could regenerate ressources of a level only after the player has replayed and finished some other levels ? Or to make the regeneration random (ie, a ressource will reappear 50% of the time after the player has finished another level meanwhile, +20% for each other level finished) ? It's only suggestions, and perhaps bad ones, or too hard to implement, but that is how I see the whole thing. Since ressources gathering is a central point in the gameplay, it is important that his mechanics are superior to pure farming.
It's a good thing you have added one condition (--> the player must have discovered X areas on the map) to some researches, but there are still too much ones wich require only ressources. It would be interesting to add other conditions, which would require not only patience, but also merit (for ex., kill a sort of boss ennemy, finish a level in less than X sec, etc.).
By the way, big piles are interesting, but it is surely faster to use the enter/grab/exit-level technique to increase our stocks of ressources.
Concerning the location of the save files, I'll wait for the next patch : it will be handier to backup (copy/paste) the files if we can play in windowed mode (unless they are updated only when the game is closed ?).
And I like difficult games too (--> how many players have finished An untitled story in masterfull mode ?... for my part, I can't kill the final boss...). I think you should increase it until most people find it to be too hard .
Don't take my commentary too seriously. I know the game is finished and that you will not modify the gameplay in great proportions from now on. The game is already good ; I just wanted to give my general impressions. Definitely, what really matters is the save files, but if we can back it up, it's OK.