Sometimes it can just be bad breeders- Holly's original breeder basically stopped feeding her mother and Holly herself- result- a very tiny fragile puppy. At 14 weeks she was smaller and thinner than some 8 week old pups I've seen and heartbreakingly uncertain of things- you can see if in the photo of her when I first had her. Even now if she gets stressed she becomes quite nervous. Always been very healthy and now although petite, she's not a teacup. My vet reassured me by telling me she'd seen smaller Cavs than Holly and that Holly was simply a 'very pretty, dainty example of the breed.' You can't argue with that!
Basically while I think it's wrong to deliberately miniaturise, it's possible that a smaller puppy will develop very nicely. Holly's 'issues' are socialisation related, because we don't think she had any litter mates (if she did, they died or were PTS) and so missed out on that puppy play thing. Perfectly alright now though- I wouldn't even consider a second dog if I thought it would make Holls chuck and major and permanent wobbly