He is rather underrated than overrated because people ain't seeing Itachis full capabilities but only restrict him to his Mangekyou Sharingan; and since people are comparing Ninjas in versus threads only by their Ninjutsu spam, Itachi is underrated indeed.
Started with his intelligence, it is more than outstanding. He has incredible strategical abilities, he can analyze every situation immediately and read his opponent like an open book. An example is that he figured out that Nagato is using a shared vision, found its blind spot immediately and destroyed it with his great usage of weapons.
Further his skills are expand themselves into every respect, he has an incredible speed with which he can outsmart the most opponents and keep up even with Naruto in his KM..
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(Bees hit with Samehada was easily dodged)
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(Itachi appeared behind Bee without he noticed)
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Above the speed with which he is forming his hand seals is incredible as well, he can do this and send out clones without the opponent is even noticing it.
If we go further, his Taijutsu skills are outstanding as well; he can keep up with 3 Uchihas and defeat them in a close combat, and this with a very young age.
His perfect usage of weapons are the next point, he has the best usage we've seen in the Manga so far; examples are his fight with Sasuke or the destruction of Nagatos shared vision with simply Kunais.
If we go on with his Ninjutsus, we can see that they are wuite good and useful too, though he is not specialized on them.
All this skills, like usage of weapons, Taijutsu and Ninjutsu be reinforced with his copy and see through ability; the Sharingan allows him to predict every movement and copy all of his techniques, whether it be Ninjutsu, Taijutsu or someone else, what is also a very good way to counter.
I don't even have mentioned his Sharingan Genjutsus, Itachis basic fighting style he uses in every beginning of the battle and which are strong enough to even handle a Sannin like Orochimaru.
All in one he is a very capable Ninja even without his Mangekyou Sharingan, if we consider his various skills like Ninjutsu, Taijutsu, Genjutsu, usage of weapons and speed, combined with his incredible intelligence and strategical skills. Enough to outsmart a lot high level Ninjas.
The Mangekyou Sharingan grants him 3 powerful techniques above; Tsukuyomi is the ultimate Genjutsu and ends the fight with a mere eye contact, only an Uchiha with the Sharingan can break it; Amaterasu is the ultimate Ninjutsu and ends the fight by a single glance of him and his Susanoo is a huge, ghostly samurai which is ultimately strong, fast and protects him from any attack and includes the ultimate sealing sword and the ultimate shield.
All in all, Itachi can in fact keep up with Ninjas like Nagato; but since people don't even see the strategical part of a fight but restrict it to a Ninjutsu spam (Amaterasu gets repelled, all Genjutsus avoid by closing his eyes and Susanoo repelled), he will always be underrated.
