2. Low Intelligence Play-through - Being able to play as a person of low intelligence really helped bolster the replayability of the first two games. They have already shown that they have the ability and brilliance to implement something like this. Read this article for a description on low intelligence in the previous games http://fallout.wikia.com/wiki/Low_intelligence_character
3. Redesign Quests - I hate the quest indicator showing exactly where you need to go. There is no sense of figuring anything out. You just follow the marker and then talk to the guy it points to. You can't just turn off the marker though, as usually there is nothing in the notes or quest description detailing exactly where to go. I would rather have a more detail description in the quest, and the notes for the quest hinting at where you should go. I would have accepted a marker showing the general area you need to go instead of the specific person or thing you need to interact with.
4. Drop Box Redesign - The Mojave drop boxes should be like an ATM for items instead of a courier service. I would think this would be easy to implement, just have all drop boxes linked so you can access all your items from every drop box. I ended up never using the drop boxes. There aren't that many in the wasteland, and if I have to fast travel to use one then I might as well fast travel to my base instead.
5. Traveling - I liked the traveling of the original games, and the random encounters. I would like the traveling to be reverted to the old system. Then they could implement random encounters correctly, make the survival skill useful again, implement caravan protection jobs (or caravan raids), and also enlarge the area that you are exploring (you could go across the country if you wanted). If they made each point of interest large enough I think this could work.
edit - fixed due to censorship.
