You would think with all the talent (Hashi/tobirama/hiruzen/minato/the sannin, naruto, the uchiha, the hyuga) that konaha produces it would be a LITTLE harder to just attack them with like 20 ninjas from the sand village. I mean, how was it not suspicious at ALL when orochimaru dressed up as the fourth kazekage and hid his face/whole body in that dumb outfit that the fourth never actually wore? You'd think one of konahas "elite" sensors would be like "something is DEFINETLY up here" not to mention half the village were put under gen jutsu by a gennin.
Orochimaru's technique essentially makes him whomever he transforms into, that being said since he was in the body of that woman nobody really knew it was Oro until he revealed himself and there was little usage of Sensory based shinobi back in the first part so that aspect may not have been utilized yet to discern enemy chakra.
Also Kabuto may have been a genin but his skills were on par with Kakashi, he wasn't any ordinary genin. He has been a shinobi spy since he was a child and then he basically went under the wing of Orochimaru. His rank was only that because he never passed the exams but he never truely attempted to. He could've just the same as Naruto could now if he desired. That being said no shinobi, with the exception of real genin that werent' proficcient in genjutsu (Naruto, Kiba) were trapped. even Shikamaru and Sakura managed to release the illusion.
Only the arena fell under the affects for that matter as well, doubt that was half of Konoha.
Hyuga clan is suppose to be the strongest in the village, don't forget them. With Choza, Shikaku as a stratege, Ino's father, Ino-Shika-Cho(who is overpowered right now), Kakashi and Gai who are kage level shinobis, Tsunade, Naruto(overpowered), Genma and his group(who could perform Hiraishin), and plenty other talented ninjas, they could deal with every village i think. The only village against it would be tough it's against Kumo
You overestimat Konoha due to the emphasis it's been shown as the main village. A Hyuuga had his eye stolen from a member of Kiri. 20 shinobi from Kumo took down the Second Hokage (I'm sorry TOBI-sama :T_T

. Although that's not significant to the village now you can see that there are special cases in every village not just in Konoha.
There may very well be Kakashi and Gai-esque shinobi in other villages. We have Darui from Kumo who many consider to be Kumo's Kakashi counterpart (in some aspects, mainly in his status as a powerful shinobi in Kumo). There are many talented shinobi in Konoha but there are equally as powerful shinobi likely to be in Kumo, Iwa, Suna, and Kiri.
We've seen Edo Summons of past shinobi taking down several with ease and they've only been defeated due to the teamwork and combine forces of the Five Great Nations and their strategies.
I feel Konoha is weaker than Kumo and Iwa in the sense of their overall foundation and if they were to fight on the war front against both of these nations like in the previous wars (they weren't allied but they were all fighting one anohter) Konoha would have a hard time/possibly lose because of the situation with Pein having severly damaged the village and rendering several shinobi incapable of fighting. Especially if every one of Pein's victims had remained dead, Konoha wouldn't stand much of a chance...however even with their forces capable after the fact they still remained crippled to some extent.