I had the base model 790cc Bonneville, which I bought new in 2004 and rode quite happlily until it was KIA in 2011. I replaced it with a low-mileage 2006 Scrambler, which I have since put a few thousand miles on.
Overall, I prefer the Scrambler. The most obvious reason is ergonomics - I'm 6'-3" tall, with long legs and the Scrambler just fits me better. Triumph says the seat on the Scram is 2" higher than the Bonneville and I'd say that feels about right. Also, the pegs on the Scram are about an inch lower than they are on the Bonneville, literally giving more legroom. The wider and slightly higher bars also contribute the the sense of "bigness" with the Scrambler, but of course that would be an easy thing to replicate on the Bonneville.
The 270 degree motor develops less peak power than the Bonneville (even the base 790cc version that I owned before) and its a noticeable difference. But since I don't do a lot of freeway riding or touring, its not really an issue. The big advantage with the Scrambler motor is the extra low-end torque compared to the Bonneville and this is more than fair trade-off for the kind of riding I do (canyon backroads and weaving through the LA traffic).