Kaplan I've had the same desire to move to a 996 for the same reasons. I often have to take my other car, due to lake of back seats in the Boxster. I also like the looks of the Boxster and of all the 911s over the years I find the 996 series to be a bit bland looking w/o an aero kit.
As for the performance difference, the full potential of the Boxster let alone a 911 can't be appreciated on the streets. That’s not to say I don’t want more power, but do I need more power? Can I put the additional performance to use on the street? Since I don't track my car it’s hard to justify the price difference in moving "up" the model ladder.
The A/C and clutch issues you experienced may have been problems with the particular car you drove as I haven't heard any gripes about them from 996 owners.