1. Spaying has health benefits, but neutering is only done to prevent specific things that may or may not apply to you and your bunny. Neutering is to prevent pregnancy, improve litter habits, reduce aggression, prevent spraying, make it possible to bond them with other bunnies, reduce litter odor, eliminate humping, etc. If you are keeping your male bunny as a bachelor and he doesn’t have any hormonal behaviors that are a problem for you, then you can leave him intact. Our male Porky isn’t neutered since he’s a well behaved single bunny with impeccable litter habits, who only ever humps his stuffed animals and never any people. If he wasn’t he’d be off to the vet to get snipped. Since you won’t know till your bunny is settled in if you might not need to neuter him, make sure you have budgeted for it.
2. Cage vs pen is really more about what fits in your home and how much of a jumper you bunny turns out to be. The important thing is to make sure his habitat is roomy and comfortable.
3. Those kits are a waste of money, don’t get one. Whether you decide on cage or pen, you can get a much nicer and more spacious one by putting it together yourself for half the money. I recommend using storage cube grids, aka NIC. They are super easy to build, and don’t require carpentry skills. There are tutorials all over the internet and hundreds of variations.
4. Other options for finding bunnies than at the pet store, or at a shelter are: Craig’s list; local breeders; rescue organizations that don’t have brick and mortar shelters. A great place to start is by typing in your zip code and selecting rabbit on petfinder.com.
5. It sound like that one you are talking about may be the dominant bunny at the store, you may find him/her to be very aggressive.
Most importantly, do not bring a bunny home till your parents are 100% on board with the idea and fully committed to dealing with the responsibilities of bunny. This must be a whole family decision, and they need to be willing to care for the bunny at times when you are unable to.