Each faction has different designs, which should serve as identifiers. Plus the HUD displays ship names, faction color, etc.
The ships v.s. screen size isn't so much of an issue now due to the resolutions being higher in this version.
At 1280x1024 fullscreen the ships will be the size shown in these shots. The ships at 640x480 are actually scaled smaller than shown here. To be perectly honest, there aren't 640x480 shots, but are cropped 1280 ones.

Tracking targets will still be a little tricky due to newtonian physics, but generally you won't be blind-shooting at an offscreen indicator to hit a target unless using missiles.
The exact amount of scaling and the speeds of ships are all things that will need balance testing tweaking.