Yes the m3 note will get the flyme 6 update, it is in beta right now, there are also some bugs in meizu phone. Btw in your title, the m3 is a completely different phone to m3 note in spec. I would suggest you to buy m3 note with a larger storage as meizu lock the move app to sdcard function for the m3 series (does not work with root).
The m5 note uses the same chip set including cpu + gpu of the m3 note, with no particular improvement in specs, but is running flyme 5.2, marshmallow and the m3 note with flyme 5.1 lollipop. If they are really the same price i would go for the m5 note just for the extra 1 gb of ram in the replacement of the 100 mAh of battery decreased. I personally think the m5 note is just a rebrand of the m3 note, just like most meizu phones.