There were no major API changes for almost all apps to maintain compatibility with El Cap except for SIP, which MS shouldn't be violating in the first place. In other words, Apple did in fact ensure that developers would not have any problems for El Cap as much as they can (excluding SIP).
99% of the apps just works fine with zero change on El Capitan or even Yosemite or even Mavericks.
Microsoft chose to remain with the older APIs and write their own custom code that's fragile by nature. They were the last major vendor to leave Carbon APIs when everyone else left it for more than 10 years.
Microsoft is a big company with a large QA department that can test their apps on beta versions to make sure it works fine when it comes out.
Microsoft is a big company but that doesn't it will devote resources to the Mac. The saying goes if there are 100 dev on office for windows, there would be 10 for the Mac. lets face it. MS has no big interest in giving mac users a good experience. they will just make it good enough so you will still pay. As long as MS is a monopoly, it will never change. What we need is another company that can compete with MS.