Neither is better, they are pretty much the same. TR3650 doesn't have a removeable bellhousing, not sure if a T45 does. The shifter may be different. Wiring harnesses for the the transmissions may be different too. I imagine it shouldn't be too much difference.
+1 That's the way to go. Beefed up 3650, direct bolt in.
All these people talk about going to the T56, but it has a taller 1st gear. So yea, it's a 6 speed, great, but less take off in 1st.