I use the S-Pen on my Note 3 all the time. If you want an S-Pen, but don't mind the new S-Pen features of the 4, you can save a ton of money by waiting until the 5 comes out (maybe a month, maybe more). Then the price of both the 3 and the 4 will drop. (The 3 already did when the 4 came out.)
The M9 is a great phone if you don't care about the S-Pen - except for the non-removable battery. No spare, no removing it if it goes into thermal runaway, no buying a $15 battery when it goes. And a Qi charging back is a lot more than a Qi receiver that you stick into the Note, if you're interested in wireless charging..