I agree with everything said so far and I'm going through the same scenario. Morgan is only 9 weeks old and given his size I decided not to have the vet do all the shots in one appointment. It's amazing to me that some vets don't seem to have a concern when it comes to these little guys. I kinda got the feeling from the receptionist, that she thought I was a paranoid mother hen. They were going to schedule the 5- or 7-way AND the rabies on the same day until I objected. They are a new vet to me and aware of the fact, that we're talking about a 2 pound dog here. I'm already not liking this.
Long story short: go with what you're comfortable with. You're gut feeling is already telling you to space all this out, so stick with it.