Looking for some opinions on this i5, XFX Radeon R9 280X, Mini-ITX build

If you're not overclocking there's no point in getting an H80i or a Z87 motherboard and there's definitely better PSUs you can buy than the Corsair CX series. What's your budget?

Change the power supply to a 500w one to save money and you could buy extra fans to lower the temps. Make sure you buy the black version of the prodigy because it Is the only one which has a large fan grill in the front. Therefore it has the best ventilation

Sorry I only just noticed you listed the colour of the prodigy! But still 600w is excessive for your build

You need a CPU with a "K" designation in order to overclock. Try something like this:

PCPartPicker part list / Price breakdown by merchant

CPU: Intel Core i5-4690K 3.5GHz Quad-Core Processor ($199.99 @ Micro Center)
CPU Cooler: Cooler Master Hyper 212 EVO 82.9 CFM Sleeve Bearing CPU Cooler ($24.99 @ Newegg)
Motherboard: ASRock Z97 EXTREME4 ATX LGA1150 Motherboard ($128.99 @ Newegg)
Memory: G.Skill Ares Series 8GB (2 x 4GB) DDR3-2400 Memory ($86.99 @ Newegg)
Storage: Crucial M550 128GB 2.5" Solid State Drive ($84.99 @ Amazon)
Storage: Seagate Barracuda 1TB 3.5" 7200RPM Internal Hard Drive ($52.91 @ OutletPC)
Video Card: EVGA GeForce GTX 770 2GB Superclocked ACX Video Card ($309.99 @ NCIX US)
Case: Corsair 300R ATX Mid Tower Case ($49.99 @ Micro Center)
Power Supply: SeaSonic S12G 550W 80+ Gold Certified ATX Power Supply ($74.99 @ Newegg)
Optical Drive: Lite-On iHAS124-14 DVD/CD Writer ($16.98 @ OutletPC)
Total: $1030.81
Prices include shipping, taxes, and discounts when available
Generated by PCPartPicker 2014-08-04 23:50 EDT-0400

You've bounced around a bit here so it's a little hard to tell what you are going for in terms of size.
If you are worried about airflow etc, then the Elite 130 is probably not a great choice as it's very tight inside and has limited options for cooling/cooler improvement.
The Prodigy on the other hand (or if you prefer something similarly sized/shaped to the Elite 130 - the Fractal Design Node 304) has pretty fantastic airflow. Avoid the side window versions if you want keep a mid-high end graphics card nice and cool, but the solid front versions aren't terrible. Ideally you'd upgrade the case fans too - back to a decent 120/140 and front to a decent 230/200/140 - two is all you need.

As an example, this is how I would do an overclockable i5+R9 280X Prodigy build. You can cut it down a little, namely by saving on the cooler and the PSU. Any solid 120mm tower cooler (in the vein of the Hyper 212) is likely to be a safe bet, I just stuck in the Phanteks as it's a great performer, looks nice and comes with a couple of decent fans (little more like the H80i in your original build). The PSU you don't want to go cheap on, especially on a build this expensive. I don't think the $90 I allocated was extravagant, but on a good day you can pick up something like an Antec HCG-620M for around $60 so there is some money to spare.

I went with the Gigabyte 280X as it's the cheapest of the three and arguably has the best cooler. XFX aren't known for producing excellent graphics cards, though the current generation of coolers look very cool.
If you have an Nvidia or EVGA preference, the GTX770 ACX is a great card so it's by no means a bad option at all.
It's perhaps worth looking up benchmarks of any games you are particularly interested in playing as despite the GTX770 and 280X being fairly similar in performance, different games will favour them in different ways.

~$1000 for an overclockable i5 and 280X is pretty much normal, the only significant omission from both your original and my build is an SSD, which is arguably a standard feature at this price bracket. If you removed the case fans and went with a cheaper cooler you could just about squeeze in a 120Gb drive which would be about as "cookie cutter" as a ~$1000 build can be (most builds would be ATX, but there's no significant cost difference here on motherboard+case).

Just for reference, here is a non-overclocking build which will look identical and perform very similarly in most games but is built to be more budget conscious. Again, it's worth checking out any benchmarks for games you are interested in to see how well they scale with CPU overclocking.
I'd still consider upgrading the case fans, and maybe the CPU cooler too, so it's not a like-for-like in the strictest sense, but this will work fine out of the box and cost $200 less.
http://pcpartpicker.com/p/8pmfnQ

As a side note, if I was going for a HTPC style gaming machine, I perhaps wouldn't go with a Prodigy, especially if I didn't need high end CPU cooler support (and I'm like the Prodigy guy, I've had three of them) as it's a bit big and awkward (the side I/O for example) for sitting in a cabinet or somewhere discreet. I'd probably go with something a bit more compact like the aforementioned Fractal Design Node 304, an EVGA Hadron Air (expensive), Silverstone FT03-Mini or Silverstone Raven RVZ01 (both expensive and use SFX PSUs). They are all worth a glance if nothing else, all have drawbacks if you need an ODD bay (none support a full size) but all are very compact and discrete.

Looks good. There's a couple of changes I'd make though-

The SSD is basically the cheapest model on the market. It's ok-ish, but I'd probably go for a Samsung EVO or Crucial M500 as an entry level SSD.

Noctua fans are amongst the best on the market but unlike the Prodigy, the Node comes with three decent fans and an integrated fan controller for them. I'd stick with the stock fans here and see how you get along - you can always change them out at some point.