I can tell you there is no perfect motherboard, issues varies from user to user, i can only share you my personal experience.
On my Asus Maximus VI Gene, i had mulitple issues some that i just couldnt live with it so i swap to MSI.
1) Audio - Realtek 1150
I had an pop or extra click after pressing any windows action, like opening a folder, or opening software, etc. Totally anyoing over time. But i couldnt go into a deidcated soundcard cause i went with a triple slot cooler for my GTX780 so was too close. This issue i blame realtek, but i tried with asus rep to use mulitple beta audio drivers, never got fixed, the issue is not that common but there were other on the ROG forums that had the same.
2) Stall at the beggining on windows
For some weird reason there was a delay upon loading, like hickup, where i lose control of the pc for like 5 sec, most of the time when the windows loadup sound is played, but since it was right there, its like the note got extended, very anyoing also. This im not sure what it was, but sometimes when the delay passed over 5sec some drivers didnt load, very common some kernel nvidia driver.
3) Shutdown sound
When ever i turn off my pc the speakers made like trumpet sound, hard to describe, like a note stayed on them and never stoped until the PC loses all power, this i woudlnt care much i just had to shut down my speakers before my PC.
4) AI SUITE III
The software seems fine, but its a overload of things that i personally dont need, this is just me nitpicking. One big issue is the way that Asus AI SUITE III measures temperatures, it doesnt match any software out there, and has been explain by Asus JJ that its not core temps, nor pack temp, but a formula that asus implemente measuring mulitple sensors and coming up with that temp, weather its accurate or not idk, but on idle was like 10C under and on load was like 5C higher, but its not linear, so i couldnt adjust to it, i commonly use core temps as my guide to know if i can run it lower or i need more cooling. This shouldnt be a big issue as long as you dont get near the max temps that intel allows. But when im cant plan my fans graph with something that i cant predict so in the end the temp measure was a big deal for me. Now asus fanXpert2 is fabulous, really the easiest way to turn down your fans, but i just wished it used the core temps and be a stand alone app and not binded to AI SUITE III.
5) BIOS fan control
Asus on haswell ROG board (not sure on none ROG boards) decided the minimum % was to be 40%, for CPU_FAN header, this is totally unacceptable when you have other manufactures like MSI allowing till 12.5%, or Asrock going to 0%. This was my fail back when i saw the temperature reading on AI suite III, and would have worked fine if it was 20%, so i made a petition that simply got ignored, so not buying another Asus for my builds until they make the fan control on bios a competitive with MSI/Asrock.
The biggest issues were the sound, but im also preparing for 4k, given that atm we dont have the GPU power to move that resolution on current games, i feel maybe in a gen or two, a SLI setup might be decent on 4k. I had a chance to test some PWM fans on the asus and liked a lot how low certain fans can go (scythe and noctua re among the best on pwm in my experience), so decided to go with BIOS fan control, and i had done a MSI Z77-GA43 build for a friend and the bios fan control was decent, so decided to go with MSI (didnt know Asrock was so tweakable on bios at the time), so went with MSI Z87-GD65, being so feed up with realtek 1150 decided to go with dedicated soundcard (omega eclaro) and i read some issues related to killer E2205 that comes with MSI, this was with old drivers, i have a MSI GT70 One laptop that comes with E2200 and it was a nightmare for 4 months, disconnects in all games, but was with some routers not all, so i waited for new drivers, and to be honest the ones relased on july were really good, i no longer have any issues with my laptop and windows 7, but you have to understand that i was really pissed by this time with all the issues that i had with Asus, so i didnt want to deal with more things, so i had a Intel CT PCIe network lying around from an old build, and it was very good for years that i used it on X58 setup, so i decided to install it to avoid any issues with the E2205, and all been perfect, i have no issues at all to say about MSI, but i didnt test the soundcard nor the network, but i will have to when i get the SLI running, at least one will have to be taken off to make space for the dual GPUs.
Now on MSI bios fan control, i cant say anything bad, aside for many a little more options in the %, but its fine how it is, give you 12.5%, 25%, 37.5%, 50%..... 100%, so you have a good amount of ranges to chose, i would have loved to see 5% increments though, as some fans can go lower and it will allow to set some even lower, but again not a big deal, at 12.5% my noctuas spin at 225rpm (they can go 185rpm but its fine as it is, barely moves any air at that speed). One great thing about MSI is that it offer 2 true PWM fan headers (CPU_FAN1 and CPU_FAN2) both are binded to the CPU temp, this was a surprise as i though was like asus wiht only 1 true pwm fan header, this allow me to setup all my case fan (noctua NF-A14PWM) to one header with a Swiftech fan splitter, and leave on the other header my CPU fan (TY150), so i have a more aggressive fan profile for CPU fan and very low profile on the Case fans. The MSI bios also allow to restrict the max on the PWM fans, so for example the Noctuas can reach like 1500rpm, where they are very loud, but with the MSI i restricted to 50% where they reach 650rpm still very quiet at this speed. One last plus of doing it with bios is that you can use whatever probe you like, i usually use coretemp and the temps and ramp ups match exactly into how i setup on the bios, so im a happy camper, all work out really well at the end.
Im very happy with how everything ended, the sound is amazing, my temps are very good, the computer has no stalls, its completely stable, the fan control is amazing, love not having extra software to control the fans. Now the only thing that i might do in my next build is to try Asrock, from what other spcr forum memeber reported has much more tweakble bios fan control, more breakpoints and less restriction.
Now my advise to you is if you fear the Killer E2205, then go with Asrock, they use Intel integrated nic (i didn't had any issues to report with the Asus that has the same 217). Asrock also seems to have 2 true pwm fan headers, CPU_FAN and SYS_FAN1 (depends on the motherboard you chose), not sure if both are binded to the CPU. At least this way you avoid the E2205, and if you have issues with the realtek 1150, you can go with dedicated sound card later on.
Just be careful into what fans you buy, if you are going with pure bios fan control go with PWM fans (4pin) that can drop low, Noctua is good for this, Scythe is also pretty good with Glidestreams/Slipstreams, Thermalright is decent so is Noiseblocker but they dont reach as low, like around 500-600 is where i was able to drop them. You will also need a PWM fan splitter to run let say case fans on one and CPU fans on another.
Now if you are not going with aftermarket fans and the fans it comes are 3pin, i would probably go with Asus motherboard and FanXpert2, its not bad as long as you accept the AI Suite III, some do have issues with it directly, i cant say i had one that i can pin point to it, although who knows, i never fully trouble shoot the my gene with all the issues that i had, i preferred to swap into another mobo. Or look for a board that is supported with Speedfan, i just never had good luck into supporting the sensors that my motherboards have had.
Sorry for so much reading, but i tried to give you my personal experience on both boards,
Good luck with your choice,
GameMi >> MSI Z87-GD65 | Intel Core i7-4790K | Thermalright Silver Arrow IBE + 3x Noctua NF-A15 PWM @500rpms| Crucial Ballistix Sport 32GB DDR3 1600 | nVidia GTX780 + ARCTIC Accelero Xtreme IV | Samsung SA850 27'' 2560x1440 | Samsung 840pro 512GB | Hitachi 7K1000 1TB | Fractal Design Define R4 + 4x Noctua NF-A14 PWM @450rpm | SeaSonic SS-860XP2
Other builds ---> ServeMi | CamMi | MiniMi | HTPCMi