Yeah, Citymapper works well for me since I live near two different numbered line stops (ones that actually have live times). I can decide which station to go to ahead of time. I also have it push alerts to me when there are delays on my most common train lines.
Citymapper may have the real-time stuff, and the UI is good, but it seems the suggested routes are suboptimal.
An example: From 220 Schermerhorn St, Brooklyn to 1 East 28th Street, Manhattan to arrive by 10 AM on Monday:
* Google [1] correctly lists 5+6 (28 mins), 4+5 (26 mins) and Q+R (27 mins) at the best options.
* Citymapper [2] choices are C+5+6, C+4+5, A+4+6 and Q+N, all of which take 35+ mins and require an additional transfer.
It looks to me like Citymapper heavily weights the distance to the first station; the Nevins St station, which Citymapper doesn't consider, is two blocks away from the point of origin, and from there you can take 4+5 instead of the C+4+5. If you move the origin slightly closer to that station, it then figures correctly.
At any rate, with Google you can tell it to favour fewer transfers, Citymapper has no such option as far as I can see.
