For the same cost you instead get units.
Sometimes some upgrades make sense in situations that call for it, like getting machine gun + regen on recon or maybe, maybe, lazarus (rez) on engi.
Otherwise just get units intead.
Coms are good at building while being able to fend off small number of raiders, and that's about it. For the same cost, units will outperform any upgraded commander and they don't risk the loss of your eco module.