Where my crystal ball is fuzzy is in what is going to happen beyond Surface 2. It is possible that there will not be an ARM-based Surface 3...that the 2 will be the last ARM-based entry-level Surface. That would depend upon the real-world experience of the Bay Trail devices. If reality lives up to the hype, I can see Microsoft producing a BayTrail-based Surface 3 and removing WinRT from Surface tablets.
That is highly unlikely except Microsoft is stupid for various reasons:
1) From performance perspective Tegra 4 already outpace Baytrail particulary in GPU performance. If you are running games side-by-side on Surface 2 and Dell Venue 11 Pro (Baytrail version) the Surface 2 is generally smoother. Now keep in mind that Nvidia is making the shift from ARMv7 to ARMv8 this year, which promises a good performance jump. Add to this the announced Kepler GPU architecture introduced in Tegra K1.
2) Going from ARM to x86 would make the Surface (3) more of a me-too device, seeing of how the OEMs flooding the market with Baytrails. You also loose the resistancy of an ARM based Windows against agains attacks from viruses and trojans, for some people certainly an important feature. So limiting the Windows tablet market to a single CPU architecture and thus reducing choice is not beneficial to the Windows eco-system. Anyone looking for a high performance ARM SoC in the future would be restricted to Android and iOS.
3) Microsofts strategic direction should always offer the option to compile Windows for ARM (thats exactly what RT is, it is not a separate development branch). If the ARM based server taking off there is a huge market Microsoft may miss. AMD and even Google investing heavily into ARM based Servers. With other words RT for Microsoft is a good test-bed as well as a strategic showcase to show potential customers "we are able to deliver Windows on ARM".
In any case, even if Microsoft decides to go x86 for Surface 3 (i would be a mistake imo, see above), it would take nothing away from Surface 2, in contrary. It would be more like:"Damn, again catched malware on my Surface 3, never happended to my Surface 2".