I got the new update on Tuesday, only put ~100miles on it so far. I went straight from stock to the new Stage 2 tune so I can't compare it to previous APR tunes, but so far I'm very much liking what I've seen.
I'm still on my stock OEM clutch, which had 46k miles on it before I flashed to stage 2, so far it seems to be handling the 93 high output torque without issue. The tune seems incredibly smooth and great throttle response. Great fun to drive, and I'm actually averaging nearly 5MPG better than I was stock (and it's not because I have been gentle with the throttle :lol
The only issue I have noticed a bit of a rough idle on cold start (after revs initially settle down, the RPMs fluctuate from about 1100 to 1200 until I drive it and engine is up to temp.) I'm still on the factory spark plugs and coil packs, so I'll swap those out tonight and see if it helps the idle. I haven't seen anyone else reporting similar symptoms, so it's likely an issue with my car, not the tune.
To answer the above question, program switching still works the same as before.
To summarize initial impressions, THIS TUNE IS AWESOME!