I am in favor of a single queue system. It allows complete control over what your planet is producing, without any potential loss.
In Gal Civ II, if a planet didn't have a starport, you immediately were wasting whatever % of production you have assigned to military production. Kaput, gone, no more. This, effectively, requires you to build a starport on every single planet, if you wanted to maintain as much production efficiency as possible.
With the current system, it allows for more specialized planets, without that nagging feeling like you're wasting whatever production the planet is coming up with by not building a starport.
Some people here have mentioned that they feel like their wasting productivity by not having a dual-queue system, when it's actually the opposite, if we're talking about the same total effective production.
If, lets just go arbitrary number here, in the older system a planet has 50 social and 50 military production, and you want to build a Farm and a Death Star. Each cost 200 production units to make. In 4 turns, you get both. Horray!
In the single queue system, your planet has 100 production (which is equivalent to the old system), and you want to build the same things. Your Farm gets done on turn two, and you reap the benefits from it for two turns until your Death Star gets completed on turn 4.
Same end result, better overall I feel. I know in Gal Civ 2 you could just not produce anything social and its production would move on to military, but if you weren't producing any ships, you wouldn't get any bonus social. The single queue system, effectively, does.
I realize that this system can indeed force you to be more micro managing in some situation, like if the political landscape changes and you need to start producing a lot more space ships. But really, war should take some time out of your schedule and re-organize your building queues.
There's pros and cons to both, and while a dual queue system certainly can work just fine in my opinion, it would need to be quite different then Gal Civ 2's for me to favor it.
Single Queue Pros: No 'forced' starport on every planet, more effective focused production
Cons: Changing queues when shifting military focus takes longer
Apologies for any lack of clarity or tangled thoughts.