Hey Sean,
It's still looking good.
I don't want to deviate from your question about preference between the two too much, but I have an alternate suggestion as well as some other ideas/feedback. Some of this is based on experiences I've had developing my UI on my game in the past month.
If the player needs to read environmental hazards and they have to read them through UI obscuring it, it might not be a good idea to have it up there. Granted you have transparency on the bars, but I still think that the full to empty states for those bars would read better as a vertical progress bar where full is up to the top and empty is at the bottom.
I'd also say for branding sake and the goal of more real-estate freed up on your screen (really important for your mobile aspirations), ditch the words "shields" and "fuel" and come up with iconography for those. It'll take up less space and you can have both meters anchored to the same position on the screen if the icons are the same size. The iconography would also help if you (can't remember if you already do) have pickups that replenish. Then you have a nice 1:1 relationship between the UI and your in-game pickups.
Having said all of this, I played it just now and I don't think the bars get in the way too much. Still it would be better in my opinion to not have them obscure where things are coming in. At first I thought all of that text on the right wasn't there, but when I finished I saw one of line of it on the screen. I think that pertains to shields. I think against your bar, it's too much information and for approachability sake, I'd personally drop all of that detail. You can show it visually, but I couldn't see what impact it had on my gameplay.
Keep up the great work and thanks for bearing with my feedback. We just got back from PAX and have had to deconstruct 1/3-1/2 of our UI because it's not quite intuitive enough. I like to think it is intuitive at a glance, but not with the amount of concentration required during gameplay, Apart from pretty screenshots for promo, the still shots of the UI don't matter too much,
Take care,
Burton