If I had to buy my first X99 mobo again, I would choose the Asus X99-E WS ("Workstation"). Or Gigabyte X99 SOC Champ. Or, an "out of band" server-grade mobo which surprisingly benches just as well as the enthusiast mobos, the SuperMicro C7X99-OCE.
Combining my two 4x8GB DDR4-3000 memory kits was a bit of an issue with an i7-5960X, could underclock/overclock the CPU or the RAM independently, but unable to run both together at stock speeds. A complete non-issue with my E5-1680-3, where everything "just works".
I've yet to see anyone report lower than a 4.3GHz overclock with any Haswell-E part - aside from those who have issues with badly mismatched memory kits, wimpy (<140W TDP) CPU coolers, or outdated/misconfigured firmware.
I still don't really see the attraction of X99 miniITX, limited by form factor to a single GPU slot and nothing else. X99 microATX is a little better, at least you can still pack x16/x16 into it, along with another slot or two dedicated to storage.