I'll preface this with the statement that I'm a complete BMW addict and have owned more than I can count... seriously, I think I've had at least 20 of them.
BMW's change in design direction is definitely a polarizing topic, and I'll be the first to say that I wasn't (nor am I now) crazy about a number of their design choices. The E65 7 series is an ugly car when compared to the E38 that preceded it and the F01 that took its place. Even considering that fact it was one of the best selling BMW models of all time. They sold the damned things by the boatload and as controversial as the design language was it did serve to inspire similar design cues in several competing marques (including Mercedes, Audi, Lexus, etc). In fact many of the design features which were universally hated at the time have become commonplace. Whether or not it was good design is always up for debate, but it was definitely forward-thinking and served as inspiration for a generation of cars.
Personally I like to think that they did it on purpose so as to uglify all of the copycats and make their next generation of more thoughtfully designed cars stand out again.
The 5 series is near and dear to my heart and we currently own 4 of them (E34 M5, E39 M5, E39 530, and F10 550). My favorite always will be the E39, but having owned 2 E60s (550 and M5) it really was a great car. I hated the design at the time it came out, but it definitely grew on me.
The 3 series always remained fairly conservative, but the E46 was one of the high points. It was the first one where the quality of materials used was in-line with the rest of BMW's models. The E9X series continued that and I've had very good experiences with those cars. My wife had an '06 330i and it was a great car. I'm currently driving an '11 E92 M3 coupe and it's one of the best that I've ever owned. I also have an '04 E46 M3 coupe and, honestly, once beyond the superficial items the two cars are more similar than they are different.
Of course I'm biased as my livelihood is dependent on fanatical BMW owners... and no, I don't work for BMW...