-The story takes place in olden times. No PokeBalls, electricity, automobiles etc. People lived in small towns where they farmed or ran stores and people coexisted peacefully, some of them befriending Pokemon and having them as pets or use them to help out on the farms.
It's an interesting idea. Certainly one that hasn't been explored thoroughly yet. I say go for it.
-How intelligent are Dark/Ghost Pokemon? Which ones are the most intelligent and could possibly speak with a person either verbally or telepathically?
Depends on the continuum. As Drapion mentioned, they're all intelligent on a level, but in the anime, it seemed like every ghost had the same kind of likelihood to be able to communicate with humans. For example, there was a gastly in "The Ghost of Maiden's Peak" that could speak, but other gastly seemed to lack this ability. In another episode in the Orange Islands arc, a haunter telepathically used Meowth as a puppet to speak with Ash and company, while other haunter... yeah.
In other words, you could feasibly state that any ghost could potentially communicate that way with human beings, but not every one does it.
-Are there any good ways to capture Pokemon other than a PokeBall? eg. keep a Ponita in a pen, etc.
Side note to keep in mind, but according to a few versions of canon (anime and I think the games), the ancients used apricorn poké balls. It doesn't mention how far back those kinds of balls go, so if you're going for something that's even earlier than
that, you could probably simply have humans taming pokémon the same way people keep real-life animals.
-Does silver have any affect on Ghost or Dark-Type Pokemon?
Nope. Nothing that's ever mentioned, at least. (Even then, silver's more of a piece of werewolf mythology, rather than general demon lore, isn't it?)
Is there a way to repel Ghost/Dark Pokemon or a way that people might think keeps away said Pokemon?
The anime seems to like using
o-fuda (or, as the dub calls them, anti-spirit stickers) to repel evil spirits. Channelers in RBY seem to be carrying these as well, and given the nature of them (the fact that they're seen as symbols of holy power), it's fair to say some people would believe these would work.
In "The Ghost of Maiden's Peak," Misty also uses a cross, but that's not much of a sign of belief that it would work against evil spirits because she goes on to reveal she's mixing ghost lore up with vampire lore.
Daylight as well. Gastly in the same episode shies away from sunlight, and ghosts in the anime don't seem to appear outside when it's sunny.
-Would it be absolutely horrible to have a child who gains the ability to understand Poke-speak?
Depends on what you do with it. Small child with the ability that turns out to be incredibly creepy? Awesome. Even a little canon, thanks to the anime. Ten-year-old/teenager with it? Possibly heading towards Suedom.
-Is there a possibility that some Pokemon might want to resist the growing control of Pokemon under humans?
Absolutely.
Can you think of any ways they might go about this?
Probably individual resistance -- such as, it attacks any human that comes near it and continues to defy humans even when captured. If you mean an entire species, it's likely that they simply migrate to an area that's less populated (a la the clefairy line). Otherwise, it depends on the moods of the rest of its species/pokémon kind, I think.