The tires are definitely a good place to start with upgrades. The stock tires a going to be pretty firm-riding, due to inexpensive materials, a flat protection layer, or both. If flat protection isn't high on your list, you can get some really supple tires to replace them that will improve the ride, regardless of the model of bike you choose. If flat protection is important to you, you can still get higher quality tires in the aftermarket (such as from Schwalbe and Continental) that should provide a better ride if you're interested in that.
Good luck!