Unlike normal Scouts, Commandos are completely invisible to hostile forces, and are also armed with hunting rifles, thus making them highly proficient not only as scouts, but as an elite light infantry force that can be used to either stiffen your own lines, or be used as snipers to take out high-profile targets at long range. Fast on foot and highly resistant to attrition, they ensure that Scouts you have trained or generated still retain their usefulness long after Ruins are no more, although at the onset of some scenarios they are useful for gathering resources from Ruins.
So the best use for Commandos, in addition to scouting and intelligence gathering, is also as a skirmish/disruption element. Commandos can be snuck into unfortified settlements, 3 at a time, and be used to kill enemy units or damage structures either as a primary tactic to keep your enemy off balance, or a prelude to a major offensive. Don't forget that Commandos like Scouts can perform counter-espionage missions: use these units to police your borders and prevent Agents from infiltrating your cities.
One weakness that these units have is that they are vulnerable to cavalry, especially ranged cavalry. So while these fast-running units can take out enemy infantry at ease, either in line (with a normal attack) or via their abilities, they are still very vulnerable if your enemy has rapid response units. Even seemingly archaic units such as China's Huangying Cavalry can knock down a group of them if they can get in fast enough. Additionally, these units are also lightly provisioned so don't expect to see them knocking down enemy buildings. Thus if you are playing in areas with vast tracts of land, fortifications, especially Bastions, are ideal at keeping Commando raids at bay. In which case, it is better to keep the Commandos back as support, and instead break out Marine Infantry who will prove to be more cost-effective in breaking cavalry charges and fortifications.
Although the the term "commando" appeared at the turn of the century during the Second Boer War in South Africa, its roots go back well into the 18th century, when Boer colonists needed security but could not afford a standing army. To solve this issue, militias were raised on a regional basis throughout the Boer nation under the titular commando system.
Boer commando units were unique in that they had a democratic structure and hierarchy, with each man being expected to arm himself, and those with farms obliged to bring their own mounts. Boer lands were divided into districts and districts into wards or wyks required to be able to muster men for the commando. The leaders of the fighting units, called cornets, led them rather than commanded them. To retain their leadership, cornets needed to retain the confidence and loyalty of the men in their unit, and that meant minimising casualties whereso possible. Small guerilla attacks and skirmishes against numerically and materielly superior foes such as Zulu impi and British infantry squadrons were thus the staple of commando warfare — very much like light infantry units in Europe during the Napoleonic Wars, or the Ranger units of the early American state. Relying on superior outdoorsmanship, the element of surprise in order to minimise losses and max out damage wreaked on the enemy in the rugged terrain of South Africa, the commandos (as the militiamen were now known) proved surprisingly effective fighters, especially during the Boer Wars to the extent that the powers of the day developed an interest in their methods, even when the Boers were eventually subjugated by the British.
Since then, recruitment and deployment of commando-styled units wasn't and hasn't been limited to the Boers alone: years after the Boer War, the Lettow-Vorbeck expedition fighting the Entente throughout Africa during the First World War used similar tactics of irregular warfare and raiding, as did the Anglo-Arab forces fighting Ottoman Turkey during the Arab Revolt. Much later, the British during the Second World War formed Commando units which were specialised in irregular warfare and support for local resistance forces in occupied Europe. Today, many nations host various infantry units that follow the same drill of the Boer commandos, either independently founded or through emulation of British or Boer traditions, such as the famed Bersaglieri corps of Italy, the United States' Army Rangers or the Russian SPETSNAZ.
- Anglo Boer War website, Boer forces