Yes, the red boxes are still there. Got the game yesterday and really liking it. It sadly has the ol' DS target demo in mind and everyone in the game seems to be 5 years too young to be doing what they're doing, but I can deal with that.
It also just 'feels' smaller, which is a result of it being on a handheld, having a low rez and thus shorter draw distance, and it trying to do things the original PSO did and not entirely pulling it off. The environments feel like little, modular theater sets, not the mysterious worlds I loved so much from the first.
But at the end of the day there's lots of loot, Mags, and people to play online with so I can't complain. Not paying a monthly fee or anything.