Yeah, you guys are flipping the right switches and pulling the right levers. I've been experimenting with activities (no rare trading though) and I've only got ~4600 merits so far.
Who are you pledged to?
Most of the things I can do in my Phantom don't earn much. Trading (not rare trading) is abysmal. Powerplay limited-availability commodities are almost as bad. "Aid & Humanitarian" missions are awful. Escape Pods are pretty good.
Basically you have to find out what the preferred activities for the given system types are. Luckily the galaxy map actually tells you that.
I got the impression that the powers award up to double the merits for their preferred activity than powers who don't have a preference for it. For instance there is this spreadsheet by
@DSS Lev floating around that says 39 merits per escape pod for Archer (I think). Well, Kaine awards me 61 merits per pod in reinforcing systems. LYR pays 3 merits per ship scan, I get 5.
Or the rare trading - LYR has a preference for rare trading in both acquisition and reinforcement systems, and pays up to 40 merits per unit if player claims can be believed. Kaine does not and pays 19 merits per unit. If you manage to trade large enough quantities it's still somewhat profitable, but not "10k merits per hour" profitable.
I reckon I could throw in the towel and haul some rares too, but I wanted to avoid that just because the earn rate compared to everything else is just busted and it must be unintentional.
I still do think some of the other activities are underpaid by too much, though.
That's the thing - rare trading seems very generously balanced for some powers, and other activities either lag behind at best or are just terribly badly balanced at worst. With Kaine, I kind of feel I drew the short straw, cause none of the activities I tried so far pays as good as the ones for other powers. But then again maybe I haven't tried all possible activities yet. I hear mining is good for Kaine, but very restricted in what you're allowed to do between mining and selling (just hearsay). Haven't tried it yet.
Bottom line: You need to find the best activities for your power, following any "fastest way to earn merits" without taking the power into account is useless.
Just my two cents after doing a few very confusing days of that stuff.