Just a few thoughts I've had over the last couple of days...
I system for lineout throws has already been discussed I believe.
Down on the Right analog stick powers the hookers throw, pushing up delivers the timing and direction.
As for the jumper I'd probably go for a Madden or Rugby08 style mini playbook from which you have 10 seconds (as an example) to choose a lineout combination. So you'd choose the numbers (just like choosing the shotgun or dime line formation in Madden). In rugby this would just be the number of players in the lineout. Then each lineout numbers would have a variety of jumping/movement options with different targets resulting in off the top ball or a maul setup. Once the hooker draws back the ball to throw you then hit one of the 4 pad options (X,Y,A,B on xbox for example) to send that play into motion. You also need to time the release of the throw and the power to hit that jumper. Maybe a final tap of the A button to tap the ball down off the top.
For scrums again use the right analog stick.
Ref calls Crouch = Move stick Down
Ref calls Touch = Move stick Right (towards opposition to make front row touch opposition).
Ref calls Pause = Move stick Left and Hold. At this point you'd hold the stick away from the oppositions direction and power up the scrum by tapping the A button.
Ref calls Engage = Move stick Right. Direction of the right stick movement on engage determines the angle the front row takes the hit. If you hit slightly downwards then the scrum might collapse. If you hit upwards then you might get folded up and lose the scrum. The ref would penalize you for bad hits and for not touching long enough or for jumping the engage call but you could try to anticipate the call to get a better hit.
Fir kicking I reckon move to a system using a kind of archery target on the field. So the better the accuracy of a kicker the tighter the rings. The center of the target is where the kick would be aiming. But the kick could go anywhere inside the outer ring depedning on pressur and fatigue (and a random chance factor too). So you could put the bullseye right on the touchline to try and gain as much yardage. But the ball might get slightly sliced (towards the outside if the outer ring) and go out on the full. So kickers with poor stats would become inaccurate and risky to kick with. Because real life rugby kicking is more a measure of accuracy rather than power. I'd also go so far ad to have tighter kicking targets for the strong foot if a player. And large targets for their weak foot. So if a player kids when moving to their right them they use their right foot and left foot for left movements when kicking. Better skilled player would have less disparity between left and right footed kicks.