Thankfully European Union pushed for MicroUSB standardization. While vendors (like Apple) can still get around it by bundling an adapter in European markets, it was enough to push the entire industry to standardize.
Still, both Nintendo and Apple still change charging port standards frequently (and not adopting the universal standards even when they're superior): the original GBA used a certain proprietary charging port, then both GBA SP and the original Nintendo DS shared a (different) charging port. But Nintendo DS Lite used another standard (looks a lot like MicroUSB but wasn't). Finally all handhelds since DSi (including DSi XL, 3DS XL and New 3DS variants) all use another proprietary variant!
New 3DS systems don't even ship with AC adapters! Not even a cable from the proprietary 3DS connector to USB type A! This means little Johnny will get between 0 and 1 charges out of the system on Christmas Day, while his exasperated mother has to go find a shop that's open during the holiday period just to charge the device.
Very surprising since Nintendo have sometimes been very good regarding backwards compatibility of interfaces on their hardware - Super Nintendo, Nintendo 64 and Gamecube all shared the same video cable (a proprietary connector to composite audio/video out via Red/White/Yellow RCA connectors)
Apple of course do it with constantly changing MagSafe variants, as well the old 30-pin iPod/iPhone connectors (and not switching to the MicroUSB standard) and chasing Firewire (and to a much less degree Intel Thunderbolt) and most recently choosing the superior (to USB2.0) reversible Lightning connector over the new industry standard, USB3.1 Type C.
The reasons for doing this appear to be mostly related control of an ecosystem to enable price gouging. (Can't really be due to increasing water resistance, as competitors show it's possible to have even better water resistance without removing any standardized jacks)