For me the pros and cons of the HTC One are:
Incredible battery life
Fantastic build quality
Very fast to open apps
Great sound quality from very loud speakers
Fantastic screen quality and DPI
No removable battery
No SD Card slot
Sense 5.0 is crummy (thank you Nova Prime)
The thing is, if removable battery and SD card were high on my list, like they are to many others, then I wouldn't have purchased the HTC One in the first place. It has 32Gb onboard, which is plenty enough for me as I don't really watch a lot of movies or listen to music at any other time than at the gym. There's easily enough space to load a couple of movies and a thousand music tracks and STILL leave a huge amount of space on the device.
The big pros for the device for me are the incredible screen quality and the great battery life in comparison to my SGS2, SGS3 and iPhone 5.
The HTC is without doubt the best phone I own, easily beating my other devices on pretty much all aspects (except maybe the HTC comes just below the iPhone in terms of build quality (and I mean 'just' too)). The sound quality is great with the Beats Audio too.
I still think you need to make a list of your own. You must know whether a larger or smaller screen size is important to you, or whether you MUST have 3Gb of RAM against 2GB of RAM (trust me, in these devices, it's pretty much of a muchness) or whether you must have removable battery and SD card. If you do, then your choice is clear.
Don't forget that in two years, even 3Gb of RAM will be outdated and in all likelihood cutting edge phones will have 4Gb or more. Sure the Note 3 is slightly more 'future proof' than the HTC One but at the end of the day whatever flagship phone you get will lose it's flagship status within the year anyway. If you are always chasing the bleeding edge of tech then you will never settle on a phone.
At the end of the day, there are options that you need to consider for yourself, like cost, screen size, removable battery, SD card and so on. If you can answer those, you will have the phone you want.
My comments in my first post still remain valid though. Make a list and flip a coin; you'll be surprised how easily the answer comes to you. Either phone will still be adequate in two years time with maybe the Note 3 being slightly ahead due to more RAM and a faster processor. However, if that scenario is true, the HTC One won't be so far behind as to lag like crazy and be little more than a pretty brick.
I could be wrong or I could be right but please note that what I have expressed is purely my opinion and should not be taken as gospel fact about any of these devices.
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