I either jumped the gun a few weeks ago when I called the new Timer app in watchOS 3 a disaster or Apple heard my complaint and has addressed it already. It's certainly the first possibility, but I like to think it's the second. Either way, the second beta of watchOS 3 is out and I've installed it on my Apple Watch.
The updated Timer app's issue in beta 1 was that it made it harder for me to create timers that didn't comply exactly with the presets Apple had created. In beta 2 they have addressed this by leaving you on the page you last used to create a timer. That means that if I go into the custom time picker and create a 27 minute timer, the next time I launch the app I'll be taken to the picker right away and not have to scroll and select it from the bottom of a long list of preset timers.
While this is better, it's also a little limiting. I'm happy because my Timer app has gone back to the way it was, but it still could be better. Apple was on the right track when they created preset timers in the first place, but they need to make these presets configurable by the user. I might need a 4, 25, 47, and 65 minute timers, but you may need 10, 22, 50, and 70 minute timers. Neither of us are helped by Apple's hard coded presets, so this good idea will tragically be ignored.
I've filed a radar for this as well, and I'm holding out hope that Apple will make this change before watchOS 3 ships in a couple months.