I prefer the stock app because I find Hangouts extremely annoying.
For me, Hangouts is slower to open, complicated to use, too easy to accidentally archive conversations. I only want it for texts as I hardly use google chat, so I stick to the stock app.
That said though, I have a strange bug which has followed me from the M7 to M8.
Occasionally, after I miss a call, the stock app misses a voicemail notification. By that, I mean the voicemail notification text comes in as read so it doesn't make a noise, and doesn't show anything in the notification bar. I don't realise I have a voicemail until the next time I miss a call and another voicemail comes through. Very annoying when you're trying to run a business and get back to people promptly. This has only happened with the stock app.