Going into this with the only prior series knowledge being that I am to catch them all. Got that part. Think I understand attack stats and trying to min/max that with natures. Beyond that, basically wondering when it's cool to stop catching a Pokemon I already have.

Or in other words, I'm trying to avoid:

1) Having a bank full of useless ass Pokemon, unless I get something for it. I wanna add them to the Pokedex then chuck em to focus on my "A" team.

2) Training one Pokemon for many hours, only to catch a copy later on that's just naturally outright better than the one I've been working on (and wasting all that effort)

Is the series just not going to do that to me? Or is there something to watch out for?

Unless you're planning to get into the competitive scene there's no real reason to min/max especially through the main story. If you want to get the perfect pokemon you'll be breeding rather than catching them anyway.

Just catch whatever pokemon you like the look of, try to get a good mixture of types in your party and you'll beat the main game easily. People generally create a separate competitive focused team after they've finished the main game.

What @petiew said is all accurate. The better natures and IV's for pokemon will only matter substantially if you are going to be playing the game competitively, and catching a good version of a Pokemon is unlikely so breeding is the way to go.

If you do want to maximize specific stats for your pokemon though for the slightly tough Elite Four definitely use Super Training before your pokemon fight a lot of pokemon and get familiar with how EV's work...or just over level your pokemon, that's an option too. :).

The game now have the dexNav that shows you how many pokemon in a given area you caught and whether or no you got every pokemon in that area.

Natures and IV's are really for competitive use and some of the post game content since you be up against AI with more balance teams and moves.

So just play through the main story of the game anyway you want and if you're up for it do some breeding and training in the post game.

Immediately. When you're just playing through the story stuff you really don't need to catch multiples of anything. If you get into competitive play, then you'll be catching a ton of the same stuff for good IVs and natures to breed. But from now to the Elite Four, that's not necessary at all.

Cool, thanks all!