1) Do your research and look for reputable breeders. If you're buying a dog from a good one, their dogs will be AKC registered, they'll have a well-sorted contract you sign, their dogs will be properly vaccinated up to the point when you take it home, they'll be knowledgeable about the breed, and obviously passionate about breeding. If something feels sketchy, it probably is. Always go to visit the breeder, look at their dogs, etc. before you plan on taking one home, so you can decide whether they're someone you want to do business with.
2) No clue. I'm partial to whippets, but they're hardly indoor dogs. I'd look at small "designer" mutts that are mixed with poodles. They tend to have good temperaments and not really shed much.
3) It depends on the breed and the dog, males tend to like repetitive play more and females can be harder to housebreak. Really though, a lot of it depends on how the puppy is raised (both at the breeder's, and after you take it home). One small note though is that it's cheaper and easier to neuter a male than spay a female.
4) It depends on a lot of things. Bigger dogs eat more, and food costs also vary with diet (kibble is fine, some prefer raw which can be more expensive, and utter morons buy wet food which is both expensive and bad for the dog). Do you plan on training with treats? How frequently do they destroy toys or other items around the house? Are worms a major risk where you live?
$200/year is a lowball price. Food + treats are likely to run $10-20/mo for a small dog, maybe a bit less depending on how you do it. Probably around another $150-250 for preventatives (heartworm + flea/tick). Then whatever you spend on toys, other accessories (crates, collars, beds, etc.), and replacing anything a puppy chews up.
Spay/neuter is going to be at least a couple hundred to have it done well by a reputable vet.
If you're buying a pet quality pure bred dog, the breeder should insist that you have the puppy fixed. Show quality dogs (that you intend to show) should be left whole because they cannot be shown if they are fixed. Breeding quality dogs are a subset of show quality, so will already be whole. Most dogs are pet quality.
Usually puppy price is the same regardless of gender, because there's no difference between a pet or show quality male or female. You can't predict whether a puppy will be breeding quality until it's an adult (and usually has some show wins), and the reason there are stud fees for males is that one breeding quality male can sire litters with many females, while the reverse doesn't really work. You can get some clue whether a puppy will be pet quality or show quality, and the latter do tend to be more expensive, but again gender isn't really a factor. A show quality male and female are equally desirable.
Breeding tends not to be a profitable venture... people do it out of love, interest in showing, or a genuine desire to improve a breed. The cost you pay for a puppy is some recompense for their time, and helps subsidize a stud fee, but realistically a breeder loses money in the long run.
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