Playing as Clan Hattori can be punishing in the 'early game' depending on how punishing the campaign AI is, especially since an aggressive and dominant Ikko-Ikki faction can really put the hurt on. The Hattori can be a great fit if you want to use plenty of Ninjas too, which can make for an interest campaign. Not just because of the Hattori's clan bonuses, but also due to the number of Ninja Hideouts nearby to capture and gain bonuses from.
The Ikko-Ikki are certainly interesting with their ability to incite religious unrest in a province and have it turn to their cause. I found playing as the Ikko-Ikki a bit less punishing compared to say the Hattori early on due to their potentially superior starting situation, you start with two Castle-Towns for one. Though the Ikko-Ikki have a bit more to them then just religious unrest via Monks, their Generals can be upgraded to help convert a province's populace to the Ikki cause.
If I recall correctly the Ikko-Ikki have access to some special Warrior-Monk units unavailable to other clans too. As for which clan I would personally recommend playing as, that is a tough choice. The Ikko-Ikki certainly play the most different compared to the other Shogun 2 clans, but I found the Hattori campaign more satisfyingly challenging early on out of the two clans.