New iMac (mid 2013) storage options
The PCIe flash storage will be faster than the SSD, but how much you'll notice that in the real world is questionable.
The PCIe card used in the new iMacs is the same (custom) stick-like form factor Apple uses in their other products.
You should get the 1TB or 3TB Fusion drive configuration if you want more than 256GB of storage and don't want a larger SSD. You could of course get an external USB3 drive to provide large storage if you prefer, or even get a USB/Thunderbolt external SSD.


The $200 for the fusion drive is expensive, but not insanely so. It will give the most noticeable performance boost of any possible upgrade on the iMac, unless you prefer to spend the money doing an all-SSD setup, which will still be very, very fast.

You're not going to find a compatible PCIe SSD for any less than Apple's upgrade cost. For example, OWC sells compatible SSDs for the MacBook Airs (http://eshop.macsales.com/shop/SSD/OWC/Aura_Pro_Air_2012) that may work, but I don't believe anyone has specifically tested it.

I will also note that opening up the current iMacs is more difficult than in the past, due to the laminating process on the screen to reduce glare, parallax and weight. It would be a false economy to buy a $2000+ computer, only to risk damaging it by opening it up for the chance to save $50. If external storage is not desirable and you want more capacity, go Fusion.