mostly I need to redo the main screen to be 3D (topview + isometric) and all the things that are related to this. (the game is OO data and graphics are separated, for good and for bad)
With customizable weapons and units it will be difficult to do nicely in 2D, too many permutations of unitas, weapons, armor etc. This would probably be better in 3D where you can add each customizable item into a units drawing function.

As I only really do 2D stuff it might be better to speak to some of the 3D guys, have a look at the engines on Sulaco.co.za as they have their own 3D engine: Rage 3D. Here is a direct link to the Rage 3D engine: http://www.sulaco.co.za/rage_game_engine/ there are other 3D engines around as well.