In the first couple of seasons, NX-01's crew was consistently portrayed as eager explorers who were out of their comfort zone in a combat situation, even taken by surprise when they found it necessary to fight rather than make discoveries.
...Of course, they were also consistently portrayed as being out of their depth in the whole exploration business. They were the first, after all.
A big deal was made of the fact that NX-01 was the first deep space exploration vessel in Starfleet service. Before that, Starfleet had apparently been doing something else - quite possibly related to the stuff all the
other witnessed Starfleet vessels did, such as kicking Klingon ass in "Expanse", riding shotgun to convoys in "Twilight", and so forth.
The possible lack of military competence portrayed by Archer's crew could easily be attributed to the fact that they sailed out for a diplomatic milk run in a vessel that was supposed to receive her armament next Tuesday. Quite possibly Reed was the only militarily competent officer aboard. Everybody else would have been there to nurse the new superengine and to run the absolutely necessary support functions; the soldiers and the scientists would have been left ashore, as Archer wouldn't have been able to drag every one of his intended combat and exploration team to the grossly premature maiden voyage personally, like he did Sato.
It was just too bad that the maiden voyage took two years without resupply or crew rotation. But that was a political necessity: had Archer returned home after the "Broken Bow" debacle, the Vulcans would probably have welded the ship to the pier...
After those two years, there wasn't a sign of military incompetence any more. And the ship was bristling with armament
beneath gunports that had always been there! Clearly, this was the level of military readiness that had been originally intended.
I'd argue that UESF before Archer's adventures was a thoroughly military organization that was itching to be more. Alas, it had no opportunity for exploration, because everything within the range of its slow vessels was already explored by the Vulcans, and it had little opportunity for combat, because everybody else could run circles around its ships, or alternately cut them to pieces unpunished. This frustrating atmosphere would have fostered conventional military discipline, rather than a more liberal Cousteau model; Archer would have been in a happy minority because he got to play with new toys in the Warp Five test flight program, meaning he'd be among the more Cousteauesque officers in the service when NX-01 finally sailed...
Timo Saloniemi