I have some 'legacy' units taking up my population cap. It would be better if I could upgrade them for my current epoch, is that possible in this game?

units are upgraded automatically to their newer version when you advance to a new epoch.
those units that do not upgrade simply have no newer version. as far as i know, there is no better option than to kill them off to free up population points.

Thanks, that explains why I still have some legionaires from the beginning of the game.

Legionaires are the unique units available only for the Roman civilization in epochs 1-5. That's why they don't upgrade to newer units. You can simply kill them by pressing "delete" button on your keyboard.

Usually all "normal" units upgrade by epochs. Only horses in epoch 10-11 are an exception - they don't convert into tanks. Same thing with ships (epoch 5, 10) - they won't upgrade to newer type.