Valjean,
I'm a Lutheran minister living in Cambridge, working at a church in Kitchener, and moving to Doon Mills area in December. We flew Southwest from Buffalo in January and left our car at the Buffalo Airport Holiday Inn Express for a week -- no problem. I would not hesitate to do it again and again and again. The hotel had an on-demand shuttle -- ready to leave whenever we wanted it. The driver dropped us off at the trunk of our car on the return trip home and we were across the border and on our way home to Cambridge in no time.
I did a very quick cost-analysis of that trip and discovered, to my delight, that our travel costs were about 1/3 of the cost of flying from Pearson -- even with staying at the hotel the night before our departure. We had a leisurely drive to Buffalo in daylight hours, checked in to the hotel, enjoyed a supper in the food court of the Walden Galleria, had the complimentary breakfast in the morning and gleefully left our winter coats in the trunk of our car.
I truly believe you will lose all cost advantage with a long distance airport shuttle service from Waterloo Region or anywhere nearby. I had no qualms about leaving our car in the HIEX parking lot in Buffalo - no difference than leaving it in an airport parking lot in Toronto or on my driveway in Cambridge.
Enjoy your trip!