The only amenity I can think of that you don't get at the villas that you do get at the lodge is a USA Today newspaper (which I never read on vacation anyway). You have access to all the same recreational facilities, the same pools, the same transportation, you check-in in the same lobby, use the same restaurants, and share the same parking lot. The villas have always seemed a little quieter to me, and I love their lobby area, with the fireplaces and game tables.
IF you decide to save money by "renting points" from an owner instead of booking through CRO, you do lose the daily mousekeeping. You'll get full mousekeeping about once per week, and a trash & towel service midweek. You also won't get resupplied on toiletries and coffee. If you book through Disney, you get full mousekeeping every day and restocks on toiletries, laundry soap (if applicable), coffee, etc.
I've stayed in both. It sounds like you have more than four people in your party, so that would mean booking a two bedroom villa. That can be very expensive going through Disney, more expensive than two standard WL rooms. If you have six people, plus one under three years old, have you checked into booking a deluxe room at WL? I would definitely compare the cost of the deluxe room against the cost of the two bedroom, if your party size will fit.