You have to think of WordPress as a tool. It is something that does a job, and it does that job differently to other tools, so there's always going to be a learning curve. From my experience it is easy and user friendly as long as you're looking for a blogging platform that you can write with. The customisation is something that's always going to be more involved no matter what you use.
I'd think that most of the problems that you have with the look of the content is that the CSS rules are either different/wrong or not set up in the new system. It could also be the structure but it's very hard to say without seeing what youv'e got and what you want it ot be.
As far as editing the home page in the theme and not in the pages area - that's purely the theme that you're uisng. A "standard" worpdress installation lets you set a normal page as the home page and you edit it with the rest of the pages. I've seen many themes that go away from this (like yours does) and I have ot admit that I think that it's a terrible idea as well. Unfortunately that's all up to who ever has written the theme, so you'd need to take it up with the themes author to find out why they've done it that way.