Hello, I will be ordering the parts in a month. My requirements are to be able to play Skyrim (and most other games really) on max settings with good FPS, to leave room for upgrades,
and to cut unnecessary costs. (I'm pretty sure I can make this amount of money when the time comes to order so I don't need to cut costs too much but if you see a stupid decision on my part please let me know)
Booting from an SSD and using an HDD for mass storage is a very common thing to do and is a great way to optimize hard drive performance. I don't know what made you pick the Agility III but I imagine it was price vs. performance. I own an Agility III and it works fine, but they are notorious for being unreliable. The best SSD right now (arguable) at around your price point is the Crucial M4 128GB for $200. That being said you can make whatever decision you think is best. http://www.newegg.com/Product/Product.aspx?Item=N82E168...
A GTX560ti is a nice card but it's going to have a hard time maxing out newer games at 1920x1080. Video cards are all about what you can afford, but you'll need more than that to max out a 1080 resolution.
A good budget gaming motherboard is the ASRock Extreme3 Gen3 for about $125. There's nothing wrong with your motherboard, but if you're ok with the features on the Extreme3, it'll perform great. Be aware, though, that it doesn't have a USB 3.0 header (though it has USB 3.0 ports in the cluster), but that's not a problem because your case doesn't have USB 3.0 on it. http://www.newegg.com/Product/Product.aspx?Item=N82E168...
If you want to upgrade your video card you can make a few changes. If you're willing to sacrifice performance in other areas you can get rid of the SSD completely. If you're not overclocking you can get rid of the aftermarket heat sink. A great budget case is the NZXT Gamma for $35. http://www.newegg.com/Product/Product.aspx?Item=N82E168...
Upgrade it to what? a GTX 570? This is good advice thank you.
I think I'll try overclocking. I like the idea of the SSD I think I'll stick with it.
On paper(details tab) it seems like the Agility III is better but if it is notoriously unreliable maybe I should go with the crucial... I don't know I'll research it.
The case that you linked (the Rosewill) doesn't use a USB 3.0 header for the front USB 3.0 ports, it uses a pass-through cable. There are two places to get USB 3.0 connectivity. You can get it in from the port cluster on the motherboard (on the back of the computer, outside the case) or from a header on the motherboard (inside the case). The "pass-through" cables basically use an extension cord to move the USB 3.0 ports on the back of the case to the front of the case. Using a USB 3.0 header, though, adds two more USB 3.0 ports in addition to what is on the back. Pass through cables work fine but they look terrible and they can slip out sometimes. Headers are superior.
Skyrim is not a very demanding game from a graphics standpoint and a 560ti will do alright and naturally a 570 will do better. I'm not an expert in graphics, but I think that the difference between a 560ti and a 570 is bigger than the difference between a 570 and a 580. However, a lot of graphics-intensive games will have a harder time on a 560ti and may even struggle on a 570. Numbers speak louder than words, so you might want to look at the Tom's benchmarks for Skyrim and Battlefield 3: http://www.tomshardware.com/reviews/skyrim-performance-... http://www.tomshardware.com/reviews/battlefield-3-graph...
Note that "full resolution" doesn't mean anything. It's about the resolution that your monitor can support. The monitor you picked runs 1920 x 1080 resolution.
The Agility III is not better than the Crucial M4. If you benchmarked them both the Agility III might max out it's sequential reads a little more, but sequential reads/writes are the least important statistic and in real applications the performance will be the same. There's nothing wrong with buying an Agility III, but be clear - the performance difference is almost identical and the M4 is considered a little more reliable and that's why the M4 is a little more expensive.
Also, as I think you may have already noticed - there is basically no difference between the Agility III and the Vertex III. The only physical difference is the brand of nand ram that they use and the performance difference between the two is within the margin of error. Just get whichever of the two is cheaper.