Being a milkshape user who thought blender's interface was confusing, went with milkshape. After a while, i relized you could do much more with blender's dts export, so i went with the latest blender and 4.49b combo to switch between the very beuriful interface, and the other with the dts export (I may fix up bhe DTS exporter if i learn the blender api a bit more, I know BGE but that isnt the same as blender's api, to work with 2.6x to 2.7x) Anyway, after using blender for a few days, i memorized the main hotkeys and found the ui to be very useful.
Give blender a shot, all it requires is a bit of learning and how powereul the tools are.
A basic rundown
G - translate
R - rotate
S - scale
and you can always use the onscreen translate arrows.
Pressing x,y or z will lock your translation to the axis.
Right click to select (you can change it to use left click, but i've gotten used to it)
Blender is the best choice for me, even though i've used milkshape the longest. You will get models done blazingly fast with blender's array of hotkeys and tools.