I'm not a Nike+ user (although I would like to be) but I may have some thoughts that can help you. I can't comment on this particular system, but I can use my extensive amateur knowledge of fitness and strength training to make educated guesses and provide you with some helpful resources.
"- although I might pick "get lean" as my in-game goal, when I log in to do the day's scheduled routine sometimes I get more strength training...is this how its supposed to work?"
Strength training is a critical component of ANY exercise regimen... no matter what your goals are. It's a myth that strength training will "bulk you up" - whether you want to "get lean" or "get ripped", you must hit the strength training for best results.
This article will help you understand common myths regarding toning vs bulking up: www.sparkpeople.com/resource/fitness_artic
"- the Nike 'fuel' point system seems useless to me, but maybe I'm missing something...do you pay attention to it?"
Different people find different things motivating. :) Gamifying weight loss can be very motivating for some people, but if this part of the system isn't motivating for you, ignore it. ;)
"- I don't quite understand the difference between "get lean" and "get toned" in the goals in terms of how that changes the workouts...thoughts?"
"Toned" is actually marketing term that has very little meaning in the real world. What people usually think of when they're thinking "toning" are silly little handweights and lots of reps... this approach is a myth (as explained in the previous article) and a literal waste of time. You can achieve effectively the same results in less time with heavier weights. :) I don't know how this would change your specific program, but I'm betting it will involve what amounts to endurance training: low weights, lots of reps.
"- the calorie burn count for a 45m cardio workout seems much lower than what my Sparks tells me I get for 45 minutes of jogging 8kms...however in the Nike+ my heart rate is quite high and I'm definitely sweating more from the mountainclimbers and burpees...something seems out of whack...thoughts?"
Heart rate estimates are always that: estimates. You can't be assured that they're accurate. THe best ones are using a heart rate monitor with a chest strap, that inputs your weight, height, and gender, and doing an activity that is well studied, like running. What's your calorie burn showing as?