I'd say keep the Prius, Audi and 4runner.
Prius: Great gas mileage and COMFORTABLE. The MR2 would get somewhat good mileage, but with no power steering, manual (I'm assuming) and being a 1993 it will not be the most comfortable commuting car. It will do fine, but sitting in LA traffic you don't want to be constantly shifting and fighting the wheel to get into the next lane. The Prius will be much more comfortable to sit in for long periods of time, the Fiance will approve of it and not give you her piece of mind every time you have to take the MR2. Plus, in the end you'll probably start a family and you don't want to deal with a MR2 and a carseat.
4runner: Pretty obvious, but it can be your camping, wheeling, snow and beach vehicle. It will hold the dogs and provide the fun and hauling needs you may have.
Audi: Simply because it's hers. The last thing you want to do is convince her to get rid of it for something you want her to have. You will never hear the end of it. I'm currently trying to convince my Fiance to get rid of her Jeep GC, but I won't do it till she is ready. You are defensive about getting rid of one of your 3 cars, she definitely will be defensive about her 1 car.
That's what I would do if I were you. The MR2 sounds fun, but your in a career, living in LA and engaged. You probably don't have the time for all the toys or to drive all 3 cars in a given week.