I love that UpLink game... its an GOG ( Good Old Games )!!
About your question:
Uplink is a 2D game. The graphics are 2D, you can achieve the same results with SDL ( www.libsdl.org/ ) But its just about the graphic interface.
The 'Big Deal' with games like UpLink is about generating random missions and/or implementing all the game mechanics ( the upgrades for character´s PC, the code to implement that 'multi link' connections... etc etc ) This code is agnostic about graphic interface.
I think you may try to implement the game mechanics first, try to think about the whole game, what mechanics will you implement in your first version, try to write it on a paper sheet, see how things will worth together and after that try to implement the code without the graphics interface.
When you reach this point - codding your ideas - maybe you have more specific questions, and the guys from this forum will be able to help you more...
Also, if you want to make a 3d version of UpLink game, so you must learn some 3d engine ( unity, unreal, etc etc)...
I will love to see a clone or remake of something like UpLink! Good Luck with your project!
( Sry if did some english mistakes.. my english is not perfect too.. )