Firmware v3.1 didn't change anything relate to battery charing.
I have charged my N6 from 0 to 99% in less than 4 hours, I consider that as reasonable with a 5600mAH battery. To achieve that, I switch off the N6 completely while I charge the device, this does make a lot of different.
On the other hand, you are correct that it take a very long time to go from 99% to 100%, this is actually a design feature to protect the battery from over charge. What happened is N6 will slow down the charging pace (i.e., limiting the charging current) once it reach a certain percentage, and when it goes to 99%, the charging current will be extremely low so it takes very low to finish the final 1% on the meter.
I have mentioned similar advice just a few pages back:
You should avoid completely discharging or full charge a Lithium battery. Unlike NiCad batteries, lithium-ion batteries do not have a charge memory. That means deep-discharge cycles are not required. In fact, it's better for the battery to use partial-discharge cycles and avoid over-charge. I'll avoid the use the N6 beyond the last 20%, and will stop the charging at around 90%, and after something like 10 charging cycle, I'll do a deep drain to the last 2% or even till the N6 die off, and then charge it up to 99% again. As RELIC has pointed out correctly, the deep discharge periodically is not really to bump up the capacity of the battery, the main purpose of that was to calibrate the battery charge level indicator. So I suggest you don't insist on getting the final 1% charge up in the N6, stick with 20%-90% as your regular charging cycle and you'll notice the charging time is a lot more efficient.
