What is your favorite motherboard manufacturer and why?

None of them. 

Most of the motherboards I've bought have been made by Asus and I've had several Gigabyte boards. The build quality between Asus and Gigabyte is almost always the same but Asus does a much, much better job with the BIOS. Asus also does a much better job with BIOS updates compared to Gigabyte. Asus boards are great when they work, but if you have to RMA the board then Welcome to Hell. 

One board that I have is a Gigabyte z370 Aorus Gaming 7 and it's a very well made board with good VRM's. Except the BIOS interface is very basic and VRM heatsink needed to be fixed due to a mounting pressure issue. 

Asus doesn't always do a good job with their midrange boards like the Prime Z370-A or Z170-A. I've have two Z170-A boards that are having I/O issues. If you go to ebay, you'll find plenty of dead X99-A, Z170-A, Z97-A, and Z270-A motherboards.

I've only owned one MSI z97 Gaming 7 and one ASRock x570 motherboard so I can't comment too much about these brands. 

And there's EVGA. I've owned 5 different EVGA boards. The EVGA boards from the socket 775 and 1366 era were really good and I heard that EVGA did a great job with their x79 boards, but they have mostly fallen off the map since then. I have the EVGA x299 Dark board and it's well made but it's BIOS and overclocking options are inferior to the Asus Rampage VI Apex board that's in my main system. 

A fair majority of the boards I've had were used boards that I bought from a Craigslist seller or I won them in ebay bids.