The motherboard is what is limiting you from making a ultra powerful gaming rig. If you want to run 2 x video cards teamed as SLI or Crossfire, as well as have PCIe 3.0, I'd check into swapping the motherboard out with one that isnt limited.
However I have yet to read of a game that requires PCI 3.0 to operate, so you should be able to get by with a powerful video card added to this system with a strong power supply to handle the additional load. Depending on video card installed, 460watts might cut it, but I like to not run a power supply at its max rating and have one that has room for additional loads if needed, so a 650watt is a good PSU for a gaming rig.
Answers to your questions:
PCIe 16x and 1x are 2 totally different connections, with 16x and 1x also having differences in bandwidth to the BUS. The 1x is a smaller width connection on the motherboard and the 16x is a wide connection. 1x connections are usually used for adding cards that are not video cards, such as USB 3.0, Sound, Network Adapter, SATA III controller, etc. And 16x is mainly video cards.
PCIe 2.0 vs 3.0 ... I have seen good gaming systems running on max settings with PCIe 2.0, however, most are running SLI or Crossfire with ultra settings with teamed GPU processing power. *That is not to say that the game can not run off a single powerful video card though with 2.0. I dont have a system to compare against for single card and max settings to give you factual info, but maybe someone else here can. Generally the system resource requirements of each game are a good indication though of what hardware specs you need to play the game at minimum or recommended specs, with recommended specs being those that you want to match or exceed in resources with. I have yet to see a game that wont play well on max graphics and other feature settings at the recommended system specs.
As far as ZOTAC brand goes. I have a motherboard and a video card of there brand and no problems. When it comes to buying any new hardware I suggest a Google search of it to see if there are anyone reporting issues with it. Sometimes the reason why prices are a deal if because they are unloading the products at a reduced cost to get rid of the problems vs a recall to fix or trash them. So with every brand and specific make/model I suggest a quick search before you buy to make sure that all looks well and not many complaints with it.
As far as getting by with cheap video cards... My one friend has a motherboard with crossfire and so he added 2 cheap cards which teamed together make the 2 cheap cards act to that of a single more powerful card ar a fraction of the price. But he would have much better GPU processing/rendering power if he had 2 powerful video cards vs 2 bargain cards teamed. He saved about $50 looking at the benchmark of the GPU processing power his system has with 2 bargain cards to that of a single powerful video card, but it is also less power efficient for the same GPU processing power.
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I would get a single powerful video card and upgrade the power supply and see where that would bring me if it were my system and I needed ultra settings. If I find that I needed more GPU power, I'd upgrade the motherboard and get one with 2 x PCIe 16x slots and add an additional card that can team with the one I have and the 650 watt PSU should be ok for 2 cards unless they are overkill processing power cards. Most dual video card systems will run fine on a good quality 650watt PSU vs a 650watt chinese knockoff that states 650 watts, but is improperly labelled to sell what is really 400watt internal guts. Good name brands for PSU are best to go with than GoldenPower or other cheapo brands.
