Just wanted to ask if the Legacy GUI System (The GUI Class) is sticking around for many future versions of unity.
The new UI System is nice, but being able to do everything through code is much more appealing to me for my purposes.
I want to know if I develop a project with it, will it be removed before long?
If you mean OnGUI, that can’t go anywhere since that’s what the editor is written with, and a visual design system is inappropriate for editor scripting (you can’t design an inspector in the scene view…). If you’re talking about GUIText and GUITexture components, those are still there for now, but I would expect to see them removed sooner or later since the 4.6 UI system makes them irrelevant. Although you can still create GUIs with the 4.6 UI system through code if you want.
–Eric
In terms of performance and ease of use, I would strongly suggest thinking about using the new Unity UI system.
As Eric said, if you prefer writing code for everything UI related, you still have that option with new Unity UI. 
Legacy GUI is staying until the entire Editor is rewritten. Functionally, it has not changed.
The new UI system is now the go-to method for ingame HUD, menus and interfaces.
Use what you want.