I played a bunch of this on a flight today and I'm really impressed with the conversion to iPad. Some parts of the UI feel improved, such as the way you do power management and how you get more info on your equipped systems. Other parts are handled really well considering the reduced screen real estate. Focusing on one ship or the other seems pretty easy and intuitive.
Weapon management seems a little funky at first, but I'm getting used to it.
Having never played this on the pc I am thoroughly enjoying this. I suck at it though. I can't even get far on easy.
Are you exploring the early sectors a bunch before going to a new one, or are you making a bee-line for the sector exit? For the most part, you want to leave a sector just before the enemy fleet overtakes it, so that you've had as many encounters as possible.