Motor in the body isn't that big of a deal anymore unless you already have lenses that require it. If you get a decent speedlight you can still have commander mode (SB900, SB700, Nissin Di866). The D3100 is quite a camera, I wouldn't hesitate to recommend it at all, but the same goes for the D90. I've owned all 3 that you mention and depending on what the usage will be you can't go wrong with the D90 or D3100, both are incredible bodies.
The main differences you'll most likely notice are:
D90
Top LCD
Dual command dials
Optional battery grip
D3100
Newer
Smaller size/lighter
More auto settings
Slightly better high ISO in my opinion
Both have 11 point autofocus, which is nice.
I'd recommend he hold each one in hand and see what feels best and take it from there. I typically recommend people get the best body they can afford to begin with, saves the step of upgrading the body when they could be upgrading the lenses instead.