is it better to have 4 units each with an extra personel upgrade each (eg 4 clone trooper units each with a phase 1 clone trooper upgrade) or just 5 units?

they both cost the same so which is better and why?

More activations are generally better.

5 units of 4 troopers is better than 4 units of 5 troopers. More activations gives you more actions per round and more unit leaders to score objectives.