This video couldn't be more right. I owned 3 E46 Convertible M3s and I recently bought a '13 E93 M3. I have a previous post (when I first bought it) complaining about my transition because the E9x is too soft, quiet, and refined. So I couldn't agree with this video more. My transition has gotten better over time (I now have 700 miles and, in all fairness, I am still in the break-in period) but if you're doing to drive the car on city streets for the majority of the time (which is what I do) then the E46 is clearly more fun.
For the OP - if you have ever driven a Porsche 911 GT3 then the best way I would describe the decision you're trying to make is essentially a decision between a Porsche 911 GT3 and a Porsche 911S, with the 911 GT3 = E46 (ie. more fun, raw, stiffer, etc) and the 911S = e9x (more refined, less accurate steering, not as loud). I miss my E46 because I much prefer a Porsche 911 GT3, even as a daily driver. Yes, my E93 is quicker (actually it honestly feels MUCH quicker - almost like going from a 911S to a 911 Turbo) but it's also less fun to drive and the steering isn't as precise. I am warming up to my E93 but I'm probably going to modify the exhaust (for the first time ever) just to get a little more driving involvement.
Good luck. It's definitely a tough decision but I would very much caution you to drive both cars for a good 15+ mins before making a decision, as they are VERY different...