The S pen is pretty much gold when it comes to notes so I can't guess why you won't test drive a Note 3 before you buy it.
As it is android you can install whatever you want but I fear you have some issue that I can only guess why you wrote you wanted a clean device with no apps. For many reasons, there is no such thing.
Whether I buy a computer or phone I do not like apps installed without asking me if I want them.
Also I don't like being tied to Google, Hotmail, Microsoft, etc
I want an independent app on my Samsung Note 3 that has a calendar, notes, & address book that I can update & swap between my pnone & pc without being tied to any other system/software.
Mozilla Firefox & Thunderbird are an example of what I want for my phone/pc
Any help/suggestions much apprecaited