Congrats on your purchase! I bought a Cross Core in the summer and have about 700 miles on it so far, mostly a 20 mile round trip commute in NYC.
After about 200 miles, all the cables had stretched out (as expected) causing diminished braking and surprise gear shifts. The front hub developed a popping noise as well. After a tune-up all was resolved, though the shop wouldn't tell me what they did to fix the popping noise - I assume it was minor.
At about 500 miles the brake pads needed to be replaced. They wore out so quickly, I feel like the pads from the factory were like a starter toner cartridge that you get with a new printer. Replacement pads from Shimano were $30 per wheel plus labor ($100 for bike brakes after 4 months, are you kidding?).
I went to brake pad university on the internet and ended up replacing them myself (very easy) with
these, which are sintered (metal) which will last a lot longer and do provide more stopping power.
Not sure if it's the same with the Civante, but while Yamaha has an amazing electric drive train, it feels like they really cheaped out on the construction and components on the Cross Core. The shifters are anything but smooth, and the brakes have always been a concern, both requiring frequent adjustment to the cables to remain functional and aligned. The headset also needed to be tightened twice so far as the forks keep developing some play, rocking back and forth.
Minor point - The stock pedals are tiny little cheap plastic things that my normal width size 11 feet couldn't get full purchase over. I immediately replaced them with
these, which provide a much more secure footing.
Lastly, the charger is a problem. It is unnecessarily large, and the cables to and from it are hard wired, making it difficult to transport or replace parts. And replace parts you shall, when the cheap locking collar assembly fails through normal use. One day you will go to disconnect the cable from your battery, and the locking collar will just slide backwards down the cable in your hand while remaining locked to the battery, leaving you to figure out how to disconect it without damaging the battery - Good luck! ;-)
This just happened to me, and I'm waiting to hear back from the dealer what (if any) warranty repair/replacement is possible - As for DIY repair, you can't find any information at all on what appear to be proprietary power connectors. Others with this problem have been told to go pound sand by Yamaha and have had to buy a new charger for $200. I hope that's not the case.
Apart from these issues, as annoying as they are, the riding experience is excellent when the bike is tuned up, and the assist is very natural. My commute is far more enjoyable than it was on the Subway, and I will hang on to this bike until at least the summer to see if I can stabilize all the 'new bike' issues and have to fix it less.