Iaito has special Iaijutsu attacks when you hit R2. It's basically the same whether 1 handed or two handed, but the animation is a little bit different two handed and your character moves twice as far forward before attacking.
The uchigatana is also SLIGHTLY longer. But not by much.
Both scale the same off dex and both have the same bleed effect. Uchigatana is a slightly stronger sword with the added benefit of dealing both slashing and piercing damage, whereas the Iaido has a faster (and cooler looking) R2 attack but deals only slashing damage.
It's up to you. I more or less main the Iaido for fun and made my Uchigatana into a fire weapon. If I could get through the game without blocking so much I'd be dual-wielding them for fun, but Uchi in left hand blocks for crap. >_>
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