That...and the ancient tactics that Havoc Squad used were most likely flash trained into the the ARC Troopers during their gestation period. Giving them a tactical advantage.
You do realise that combat tactics and methods used by special forces haven't changed much since WW2?
The only real changes that have happened are equipment and weapon based.
Given how little offensive and defensive tech has changed in just over 3,500 years in SW, the tactics of both Havoc Squad and a squad of ARC Troopers would be almost the same.
They've both fought similar types of enemies and in the same kinds of scenarios.
Not to mention that there's no advantage to having flash training over traditional training when dealing with two groups of hardened special forces squads.
The whole point of the flash training in all clones was because of time constraints. Their accelerated growth rate, and having to have them combat ready in as short a time as possible.
Victory would be decided by their combat experience.
The biggest problem with this thread though, is when comparisons are made that use game mechanics of the Trooper and companions.
Look at Jace Malcolm (Trooper from the trailers). He was both Commando and Vanguard, so either Havoc Commander (we the Trooper) is both, or is one or the other with access to all abilities (non-passive and no ammo type based passives either) in the talent trees of the respective AC.