I remember the hoohah over the app spacing upon iPad unveilment. I think it is very aesthetically pleasing (6 icons in the dock aside). People wanted it cramped in like the iPhone, which absolutely doesn't make sense for an iPad. I mean, seriously, People wanted like 8x10 apps or something?
I think the spacing is really pleasing.
Yeah, I guess it can get in the way, but it's not a huge problem for me. I don't push the home button by accident due to placing much. But really, I could make your exact argument but for the opposite. I use my iPad in portrait most of the time and only go to landscape when an app forces me to (or I watch video or view landscape photos). Reading feels more natural in portrait for me. But I get why you may not like it.
My bigger beef tends to be speaker placement, particularly on iPhone. For whatever reason, they always put the default landscape mode with the speaker at the bottom, meaning it's easier to coverup with your hands. Annoying for games, and especially when they don't use autorotate.
Again, just a personal beef. My brother hates it being on the top, because apparently he holds it such that he blocks the top part.