Yes, some of the small name companies might scrimp on additives, but that doesn't mean you have to stick with big name oil companies. You just have to be smart about which ones you pick.
Depending on where you are in the US, SuperTech oil (Walmart's house brand) is made by either Warren or Shell. Both have consistently shown to be a high quality oil. You can use them with confidence.
If you look at websites like PQI America, you'll see that other house brand oils are basically the exact same (Warren supplies house brand oil to a lot of companies), and that they're equally good.
NAPA's house oil is made by Ashland, the company that owns Valvoline. They acknowledge that their NAPA oil is slightly weaker than their full Valvoline line, but tests have shown that it's very close and the NAPA oil is very respectable. Again, you can use it with confidence.
When going with smaller oil companies or house brand oils, it's not about avoiding them all together, it's about being smarter with your selections. O'reily's, Advance Auto, AutoZone, etc, they're all big enough companies that they don't want to ruin their reputation with really bad oil. Again, check PQI America (
http://www.pqiamerica.com/Feb2014/consolidated5w20ALL.html), and you'll see that a lot are very similar, and aren't bad oils at all. The small oil companies you should avoid are mostly the really small ones that you've never heard about. Explorer the PQI America website and you'll see that most of the oils that fail testing or are really bad, are from small companies you probably never heard of.
Also, unless you have a specific reason for doing them, 3k miles oil changes are wasteful. Modern oils can go significantly longer than that. So start with a quality oil, and try going 4k miles, if you're comfortable with that then bump it up to 5k miles. Again, unless there's a specific reason not to, I'd have no qualms with running SuperTech, NAPA's house brand oil, or lower price conventional oils like Mobil Super 5k for 5000 miles. They have consistently shown that they are quality oils that are up to the task at affordable prices.
As for filters, yes NAPA Gold filters are very good. They're made by Wix, which makes excellent oil filters.
Lastly, I agree with sticking with OEM fluids for the transmissions. I also agree with doing a drain and fill every 15k-30k miles. Should keep your transmission protected and running smooth for a very long time.