It's ironic that everyone is using Hashirama's cells to live forever, whereas Hashirama, the most powerful ninja during his time supposedly died during some random battle (and it wasn't even against the Uchiha...).
It's ironic that the Senju were supposed to be the most powerful clan, yet in the current era, we haven't encountered a single person with the title 'Senju'.
It's ironic that Naruto's father was a genius and his mother was a great ninja with special chakra but yet he was a dropout who failed in the academy 3 times.
It's ironic that Minato and Kushina had so many good friends and comrades but none of them thought to look after Naruto or even interact with him after his parents died and he was an orphan (except Hiruzen).
It's ironic that Naruto spent 3 years training with Jiraiya and got a minimal power up, yet after 3 days with the frog sages he became the strongest ninja in the village.
It's ironic that the strongest ninja (physical strength) in the world is a female and a medical ninja.
It's ironic that the most artistic ninja (Sai) had no emotions or feelings.
It's ironic that Shikamaru lost his match in the Chuunin exams but was the only contestant to become a chuunin at that time.
It's ironic that Konoha's strongest shinobi (even powerful than the Hokage) is a genin.
It's ironic that Sakura is one of the best medical ninjas but spends half her time injuring Naruto.
It's ironic that Naruto was the savior of Konoha 3 years prior to the Pain incident -- when he stopped Gaara/Shukaku -- but wasn't praised to be Konoha's hero until the village was in ruins.
It's ironic that Naruto understood everyone's emotions better than anyone else (Gaara, Sakura, Neji, etc. in Part 1) but was completely clueless about Hinata.
It's ironic that over 40,000 ninjas have died in the war yet they haven't killed a single person on the enemy's side. The only things they have done is sealed Edo Tensei zombies and killed clones of Zetsu.
It's ironic that Madara defied the Edo Tensei but Tobirama, the creator of the jutsu, could not.
It's ironic that Hanzo detested the samurai and their ways, but ended up stopping himself as an Edo Tensei zombie by way of seppuku (a samurai tradition -- suicide by disembowelment).
It's ironic that the current war is a result of the Hokages' shortcomings:
1st Hokage's failure to kill Madara
2nd Hokage's ill treatment of the Uchiha
3rd Hokage's failure to kill Orochimaru
4th Hokage's failure to kill Obito (not too sure about this one :x)
That's all I could come up with for now!