The Surface Pro 4 seems to have a leg up on the iPad in the stylus department, being that it's included and has an eraser and clip. I really wish Apple had gone further with their Pencil... But I really just don't enjoy Windows, and I enjoy it even less on tablets. I find it to be generally very unintuitive and clunky, but I just upgraded my Boot Camp to Windows 10 so they may impress me. From everything I've seen it makes much more sense to expand a tablet OS than downsize a desktop OS in terms of usability and functionality on large tablets.
I'd say the two styluses make different trade offs. I do like that the surface pen has the eraser/button. However, the lack of recharging at all (go buy one on a yearly cadence I guess?), and the fact they won't talk about the input beyond pressures is worrisome. Apple's input for tilt and direction is a plus for more natural input if you want more than handwriting input, and I don't yet know where the two come out in terms of input lag yet, it could go either way, but 240Hz sampling is a bit more frequent than the best Wacoms, and Microsoft hasn't said anything about their poll rates.
The Surface pen feels more like a handwriting/note focused tool, while the Pencil feels more like an artist focused tool. Neither really hit all the marks for both.