Assuming they use the same flash memory in a potential Skylake mini that they are using in the current MacBooks, read/write times would be significantly improved. When I compare my 2014 Macbook Pro to my mini, the Pro is certainly faster though by maybe 1 1/2 seconds, so for me it is not significant. I am not regularly doing heavy read/write options though and from my experience people who do have to perform such operations are quite happy with the faster drives that Apple has been using in the 2015 MacBooks.
As far as CPUs go, Skylake is more or less an incremental upgrade of what was already an incremental upgrade. Skylake CPUs are certainly faster than Ivy Bridge CPUs and burn less energy (not as much of an issue in desktop computers) but only marginally so. A Skylake dual-core i5 is not going to be the deal-maker to help you run programs and applications that an Ivy Bridge CPU cannot. In real world use it might be able to run those programs slightly faster (if we're talking something where you'll even notice CPU speed like processing work).
I do not believe the 2012 Minis are a bad purchase right now and will most likely continue to be a good purchase throughout 2016 and into 2017. Unless Apple radically departs from the design direction they appear to be heading in, the 2012 Minis will remain a better buy than the Minis for the next several years. The new dual-core machines compare quite favorably to the old dual-core machines but the quad core Mini from 2012 will most likely be a top performer on this model for some time to come.
One major issue is in graphics work where the HD 4000 in the 2012 Mini is only getting older and the Iris chips that Apple is using in the higher end 2014 Mini (and likely higher end configurations of a 2016 or 2017 Mini) are a significant upgrade. The HD 4000 is quite capable of running a desktop environment at high resolution and includes multi-monitor support but it struggles with 3D work, especially on software that is newer than 2012. I rely on mine for gaming and it is a fine chip for Indie titles and older games but falls apart with virtually anything new. The last major release I have played on it with a reasonable frame rate and visuals was Borderlands 2, though I am sure other gamers on this system might have experience with newer titles. I'd been thinking of trying Fallout 4 on it but I loathe the idea of playing that game on low with a resolution below 1080p just to get playable FPS. It goes without saying that if you aren't planning to run these kinds of programs, the HD 4000 should remain adequate for the next couple of years. This chip is capped at 2k resolution (2560x1600 IIRC) however, so if you are planning to upgrade to 4k+ in the next few years you will want something newer.
My personal plan is to keep my Ivy Bridge mini until 2017 when cannonlake becomes widely available. Unless Apple does something really surprising with the minis (like offering user upgrades and quad core CPUs again), I'll likely retire it for an iMac. I don't figure on it being a bad computer in 2017, but I will be looking to upgrade from that HD 4000 to at least a 4k display. I'll probably turn the computer into an HTPC or give it to my parents after that.