I think it's the best decision to go with a 5 speed MT. I think it's more fuel efficient than any automatic transmission and you'll safe a lot of money on maintenance costs (many automatic transmissions need oil/fluid ever other year).
Nissan had some problems with their CVTs from Jatco, but that was a long time ago. I don't know how it's these days. I'm reading a lot through some Honda forums and the CVTs of these days seem very durable and reliable. When there is failure, it's mostly due to neglect and abuse (racing and brake-boosting, not the stuff we Hypermilers use to do a lot). It's important to change the CVT fluid, but that's also important on any other automatic transmission as well.
For anyone who is curious, here you can see how the CVT of a Civic keeps the RMPs.
Normal acceleration in a city situation:
https://youtu.be/fIkoOWz3yVA
Slow highway speed coasting:
https://youtu.be/oJM7JqxiNFU