I think the most notable difference is the 2.2 with more usable power. The rest of the differences are so slight regarding daily driving if your not driving like you stole it that is.

Both are good. The Newer the model, the more refined it is. If you are not able to drive the car like you stole it, likely the AP2 is the way to go.
I have had them all and just picked up a 2001. FWIW.

I 3 season dd my '06 vsa ap2, 40 mile each way commute (and I'm 50, old but not ancient). The extra torque of the ap2 and subtle refinements of newer model are welcome attributes for this use.

I drive my S about 80 + miles a day, my drive one way is 39.5 miles, 40 mins to 1.5 hrs depending on traffic. I love my S. the hardtop made it much better though.

I might be in the minority here, but I'm glad the S isn't my daily driver. I used to have an RS4, followed by a 335i. I got rid of both when their warranties expired. I also grew tired of a stick shift as I live in Philly (in the city, not the burbs) and the traffic sucks. Most drives, I felt like I rarely got passed third gear. My DD is now a new IS350 F-Sport. It's not the type of car that makes me smile. But it's fantastic on commutes and an amazing highway cruiser. Put it in S+ and it's firm, solid and nearly silent at 80 mph. The tach is very low and it easily puts the miles down.

In stark contrast, the S2K is a smile machine. When I drive it, I'm grinning the whole time. But on the highway, I tire from the high revving engine and wind noise after about 30 minutes. It's not that different from when I used to ride crotch rockets. A blast on the back roads, but I'd find myself getting tired after a couple hours. And whenever I rode on the highway, I felt like a needed a break every half hour. Granted, the S is worlds more comfortable than crotch rocket, but you get the idea.

I don't commute, but I did take a neighbour for some eye treatment twice the last 2 weeks, 56 miles each way in peak hour traffic one way. She suggested I drive her new auto Ford Fiesta. That horrible thing almost destroyed my gammy right knee in 50 miles. Coming home I had to stop & walk around a park for 5 minutes.

Second time I took the 2001 AP1. At the worst point, a couple of miles of stop start every 3 or 4 car lengths was getting tiresome, with the starts with the low torque engine, but apart from that, it was nice driving all the way.

I regularly do a 650 miles interstate trip. This is down a good country main road, with just very occasional twisty bits. I found in the S I'd had enough after about 400 miles. My Triumph TR8, the one with the 4.6L Range rover engine in it, is the best car for these trips. With it's slower rate manual steering it will waffle down the road with much less attention & concentration, just a hand resting on the wheel, but is still enough fun in the twisty bits to wake you up & get the blood flowing again.

I would reckon you would find 4 to 6 hour trips fun in either S, but the VSA would be good if you then to lose concentration on those trips.

I don't understand this low torque business with the AP1. Never go below 4k rpm and your good.

Finally someone who gets it.

AP1 vs AP2 for daily, they drive the same. Pick the car that you prefer (looks, age, features like VSA). The difference between AP1 and AP2 is small enough that it makes comfort a non-factor.

I'd shoot myself if I had to commute in my S2k. And I'm talking about a 06 AP2 all stock. Weekend duty only - but then it's all smiles.

4000 RPM take offs every 3 or 4 car lengths can get a bit boring to after the first 50 or so, & they definitely do not like rolling on at 1500 rpm & less.

Apart from that I have no problem. They actually are not all that low in torque compared to many of the European & Japanese sports cars that came before them, it just feels that way compared to their top end.

I love the way they can putter quietly around town, so no one notices you, something I most definitely do in the V8, no matter how slow I go.