This is going to greatly depend on the country, and to an extent, the airport. Perhaps even also the flight, airline, and time of day.
For an attempt at an Australian answer, the e-passport gates here are currently only available to passport holders from 8 countries (Australia, New Zealand, US and UK included). They're planning to expand this (including through trials) to other nationalities.
Because of this, if you come in on a flight - or at the same time as other flights - that have a lot of other nationalities on them, you may find the e-passport gates are faster (assuming you qualify of course)!
The key is going to be which line is shorter. I'm not sure if the e-passport system in other countries is the same, but in Australia, you need to line up at an e-kiosk machine to get your passport scanned, answer a couple of questions, and receive a paper ticket which you insert into the passport gate later on (after which your face gets scanned).
At some Australian airports (at least Melbourne and Sydney, but possibly others too), these kiosks are placed systematically alongside the route you take to walk towards passport control (alongside the duty free shops, etc.).
People who haven't used the kiosks before line up at the first several they see. Each time I have returned to Australia, this has resulted in long lines at the first few groups of kiosks, whereas if you continue to walk right past towards passport control, you'll find many free kiosks directly next to the passport gates.
Therefore, depending on the factors I mentioned earlier, the answer in Australia is often either:
- both the e-passport gates and the manual border control take a similar amount of time, OR
- the e-passport gates are much quicker if you bypass the first few groups of kiosks you see