I assume Apple sees the need to visit the App Store as a feature. I don't think this is going to change.
Operating systems have traditionally included the bare minimum to cover many popular use cases, but the included applications are rarely best of breed. TextEdit.app/Notepad.exe are lousy text editors, Calculator.app/Calc.exe are lousy calculators, and Chess.app/Winmine.exe are lousy computer games.
I've personally never needed two timers at once, and I can name a dozen other "basics" for me that I'm sure wouldn't be in your list. We like to complain when Apple doesn't include a feature (it's so basic!), and we also complain when Apple does (they're killing indie developers!). I think this is a good one for a third-party app. Unlike, say, keyboards, there's no real benefit I can see to this coming from Apple.