Happy Surface Pro 4 Owner here
I can sort of understand the Pen not being included here. I have a Surface Pro 4 i5/128/4GB (bought personally) and it is well-made and very portable. I also bought the Type cover keyboard (actually got it "free" due to a £100 discount offer at the time) and cannot understand why this is not bundled.
I have hardly ever used the stylus (or indeed the touch screen if I am honest) after the first week of having it - for my use-case it does not warrant the cost of buying it separately. YMMV of course as I am not a graphic designer or professional photographer. I thought that I would use it for handwriting meeting notes, but after trying it once, that has never happened....
Resume from sleep can be problematic, that is probably the only gripe.
I also avoided paying for the Surface Dock (£160?) by getting a Dell external monitor which has 5 USB ports on it which was not a million miles away from that price, and plugging everything in to that (including a USB to Gig Ethernet adapter).