Warm-ups that seem a little "soft" is something that I've also witnessed, especially with wrist/back/shoulder stretching. I feel it is very important for Aikido students to properly stretch before and after class, doing so prevents injury. My classes usually involve about 15 minutes of "warm-ups" that include stretching and ukemi exercises. I've found the "warm-up" exercises not only help prevent injury during class, but also get the students in the right frame of mind (meaning that they are in the dojo now, and are ready to begin training).
I prefer to keep my general physical conditioning (weight-lifting, aerobic exercises, etc.) apart from my Aikido training. Of course, Randori can be quite the aerobic exercise in itself