It sounds like there may be an issue with your index, it shouldn't re-index every time you open a brain. You may check what your settings are for refreshing the web index (Options > Preferences > Search).
There is a thread on the active thought indicator, they stopped the rotation when the plex is not active (the mouse isn't moving on it) to save cpu cycles. Several of us posted there and asked for an option to move when PB is active. Other than that, it is slower than 3x. They are still optimizing things, at least in the 4.2x version (which had slowed down a bit more from 4.1), but if the cost of the speed loss outweighs the added features in 4x for you, perhaps it would make more sense for you to stay on 3. I disagree with your bloatware comment. The added features in 4.x actually started me using PB again. In my case, PB 3 was nice, but were missing some key factors to make it an everyday tool. But that's just my opinion, and we all know what they say about opinions...
Java SE 6