The hardware is fine today, but a year or two from now with far outdated software, that might not be a good combo. If you're planning on going deep into customization, third party developer support could fall off imminently too because most versions could not be modified in the traditional manners and most Samsung phones since that one couldn't be at all. For the root/ROM community, only the Nexus lines and perhaps the OnePlus 3 can be recommended. It's almost never going to be a good idea to buy a two year old phone if you're planning to use it as a daily driver for any length of time.
I'm quite the opposite of @nahoku; my PC is the oldest tech I have that I run as a daily driver and that only works because it has a new GPU, new SSD, new RAM, etc. PC's can be kept longer because they're modular and the components can be updated. Both of my daily use phones were released Q4 2015, my tablet was released Q4 2015, my wife's phone was released a month ago, her tablet was released 2014. TV's are all new since 4K sucked before last year, etc, etc.
The OP mentioned keeping the software up to date. Assuming, based on the decision to keep the Note 3 until Q3 2016, that this phone needs to last 2-3 years, the only phone that can be recommended from the Nexus and OnePlus 3 is the Nexus 6P. That's the only phone out today that will have any prayer of relevance in 2018 and 2019. Otherwise, the smartest move would be to wait a couple months for the Nexus Marlin, which will have 2016 specs and software that will be running strong in 2019 without issue.