I think something that would be cool would be a weapon breakdown. And crafting system. The did the weapon grinder thing but it was very limited in what it did. What I would like is a means of combining multiple elements of weapons. It would allow the weapon brands to be unique, each having their particular gun style (eg. Large clips for bandit, increased power for jakobs, elemental for Maliwan,) but then the player can break the weapon into parts.
So you take a Malian weapon and destroy it, and get back parts, let's say Maliwan flame core. Then you take a hyperion weapon do the same and get the aim correction modulator (these are just made up names) and then the Dahl high rate rat tat tat..erator... or whatever You apply these elements to let's say the frame of an SMG. And you have a custom made SMG with high fire rate,that increases accuracy and does high fire damage.
Increased movement options (eg climbing) , more fast travel locations and armor loot and player customization would all be excellent additions as well as has been stated already on this forum.
Borderlands has been perhaps my favorite game franchise of all time, and is by far my favorite franchise to play with friends and I really hope that when they do release borderlands 3 that the changes they make only serve to enhance the experience I've had with the series thus far.