Your disadvantage 1 is the result of a failure of imagination. The vast majority of life on Earth is built from nothing but carbon, oxygen,nitrogen, hydrogen, etc., and human life requires not much else. We could easily subsist on just these elements.
Note that "hydrogen" lists among your rather crucial elements necessary for life, and does not feature in Venus' atmosphere in significant quantities.
And, more so, while human life per se requires very small amounts of non-carbon, oxygen, and hydrogen elements, human technology requires very large amounts of non-carbon, oxygen, and hydrogen elements.
AFAIK, sulphuric acid is present in the Venusian atmosphere in large enough quantities to cause obscuring clouds. Though, I imagine that equipment to harvest the hydrogen from those clouds would end up being quite expensive. (Given my limited chemistry knowledge, I'd guess that large amounts of silicon would be involved in their manufacture.) There are also significant amounts of hydrogen sulfide. (Which could be quite a complication for human settlers as well.)
EDIT: FTFA -- "Moreover, while both planets boast ample amounts of volatile life-sustaining materials like hydrogen, carbon and nitrogen, only Venus’s dense atmosphere would be helpful in shielding human colonists from the harsh assault of solar radiation."
'Subsisting' does not include 'artificial cities floating in the sky'. Similarly, getting a computer to run on nothing by carbon, oxygen, nitrogen, hydrogen and sulphur, none of which are metals or semiconductors, is a massive task, if doable at all.
I don't think getting things from Venus orbit down to human friendly aerostat altitude is going to be an insurmountable problem. When sending things into the Venusian atmosphere, you can always take advantage of aero-braking. Then, the aerobraking equipment can itself be taken apart and used.
Running an economy on mostly carbon, oxygen, nitrogen, hydrogen, and sulphur would make for an interesting hard sci-fi book!
Any real colony needs to be mostly self sufficient (hopefully entirely self sufficient) so the problem is not getting materials down from orbit, but up from the surface.
In a far-seeing, long term analysis, I don't think we should limit "colonies" to discrete heavenly bodies. Long term, we should consider the complex of Venus, Mercury, and Venus-crossing asteroids as a local resource pool.
The notion that a single planet has to be largely self-sufficient as an independent unit is a bit of prejudice that comes from our upbringing on Earth. On Earth, in terrestrial economic terms, it's generally relatively expensive to get things off the planet and back onto its surface in one piece. For this reason, we think of planet Earth as a practical (if not absolute) boundary for economic transactions and resources. In the larger context of a solar system spanning society, it's costly in absolute terms by current-day Earth standards, but in the larger context, it's also relatively cheap to ship things down into the Venusian atmosphere from Mercury, Venus-crossing asteroids, and even Mars. In fact, one can make it materially inexpensive by applying lots of energy, which shouldn't be nearly as expensive by that point.
It's probably true that Earth's gravity well will limit trade of material goods between itself and the rest of the solar system. But there's no reason that a solar system spanning culture couldn't exist as a largely separate entity. I suspect people will live out there just for the idea of it, and that nation-states will help in the endeavor just to propagate their own cultures.
Right. History is full of land-based powers that didn't realize they needed a navy until they enlarged their context. This just involves an even larger new context.
Sure.. except, nature has conveniently put those elements into forms we can use. So until we're able to do that ourselves, that's a disadvantage we'll have to deal with. It's less a failure of imagination, and more a failure of our current level of technology.