Ah, mate...you've asked the hugest question that's been on my mind since I got my Scrambler in October!! I managed to keep my Bonnie, thinking that the riding quota for each would tell the tale, and so as far as that goes, I've done 4000 ks on the Scrambler, 500 on the Bonnie since then. But that's not really the whole story, as the new bike mystique and running-in and fettling requirements have dictated a bit, and the Bonnie needs some tuning and maintainence right now.
I ride a bit with a mate on a new T100, and it's certainly faster than the Scrambler, but not as versatile or nimble, and he gets snaky when we get into rough stuff, Scram eats everything. Scram's got more torque, and an easy lazy motor that just pulls anytime from anywhere; also I think she's a slightly sharper handler, certainly on narrow winding mountain roads, and is easier to chuck about, quicker steering (different geometry) But the Bonnie is a slightly better open road bike, lower, you can tuck in, and revs easier at the top end...
I'm a mess, can I keep these 2 creatures happy? Will I have to choose? There are a zillion imponderables and nuances between them, but I can't bring myself to get rid of either, that's sure. One thing though, they're very different beasts. Maybe you should get both..??
I'll leave it there for the minute, there's another guy with both bikes, Scrambler900, on this site, his opinion might be helpful - cheers, Pat