Realizing this is a bit of a long shot, but here are a few of my initial thoughts to resolve a number of issues, not just pay (but very much attached to it).
TL;DR: Change the way rank is obtained, make payout and rank increases mostly tied to missions as opposed to raw value and reward the player based on their time invested as opposed to the value of the thing they were doing.
Ranks and Rank Points:
Ranks would be changed to no longer be based on funds earned (for trade) or only ships destroyed (rank vs. rank), and would be heavily influenced by mission completions.
Ex: Harmless -> Mostly Harmless would be 50 rank points. Completing a Harmless mission would provide money from the faction, faction reputation increases, and now rank increase of (maybe 10 points). Mostly Harmless mission would give 15 Rank points, etc. Deadly->Elite would maybe take several thousand rank points, but Elite missions would give a hundred or so, etc. There would be a monetary conversion of rank to pay in the event the player can no longer obtain any additional rank. Ex: 50 rank points would be worth 5M or something like that.
Optionally, but recommended: Make this change retroactive, so (for example) those who effectively exploited via Fleet Carrier trading and are currently Elite in trade with zero work would be knocked back down to their ACTUAL rank based on the new system. Unlocked permits would probably have to persist though, due to current player locations, but if possible to kick them (and all stored ships/modules) out of the system to a nearby station then probably better also.
Missions and Pay:
Missions would be locked based on player rank, but are now the most effective way of increasing rank. Mostly Harmless pilot could not take on an Elite mission (but maybe allow +1-2 ranks above). Payouts should be a combination of their current payout + Rank increase. Rank increase would be a set amount based on the mission's rank for that category. Mission pay would be effectively flat based on the mission rank, but in general would be increased by a lot more than what missions pay now. As stated above, if the player is already Elite and doing an Elite mission, they'd get the maximum payout. The goal is to reward the player for time spend, as opposed to what they were actually doing.
Combat Ranking and Pay:
Get rid of the Rank vs. Rank increase system (and tone it down, jeez - it's a slog right now).
Rank increases from destroying enemy vessels would be subject to the target's rank, and would have nothing to do with the winning pilot's rank, subject to diminishing returns against the same player (for PvP anti-exploit purposes, reset over time).
Bounty Hunting Pay would involve a scaling based on Base Amount * Rank Modifier.
Ex: Your base bounty hunting value from a trip to a belt was 2M Credits. If you are Mostly Harmless, you're going to get maybe 2M from that. If you are Elite you're going to get 50M+. Thus being rewarded for spending the time to rank up, and also balancing new player payout so they don't qualify for Elite-like payouts.
As a new player, you still get rewarded for destroying Elite-class vessels by the faster increase in rank, and of course Elite class vessels would naturally have a higher base pay as well.
That said, mission stacking 5 missions for "Destroy 10 ships" should go into an accumulated destroyed count.
Ex: Player picks up 5 missions to destroy 10 ships each. They now have a destroyed ship count of 0/50. If they destroy 10/50, they can fly back to the station and turn in one of the missions, and now have 0/40... etc
Again, the best way to get rank would be missions, however.
Naturally, Xeno missions and NPCs should have the highest value for payout. I can't imagine obtaining 2M (base) + Large Rank increase for a Cyclops kill as being out of the realm of possibility, and of course when a player hits Elite, that Rank increase would instead translate to additional bounty pay (10M+).
Trade Ranking and Pay:
No longer based on credits earned. Ranking would be based on mainly mission rewards, and items handled.
Ex: Mining Painite would give the same per-item rank increase as mining Oxygen.
As for monetary compensation, the mission payout should scale based on the item mined and the rank, where the rank would determine the number of items required for the fulfillment.
Profits from items sold without missions would work the way they do now (of course with adjusted values, and heavily reduced values for the bigger items), but doing a mission would work similarly toward greatly increased pay involved by the faction, and rank increase.
Mission pay should be increased by quite a bit (no more of these "Deliver 5000 <item> for 3M credits). This would keep people who just want to casually mine and sell happy, but with reduced rates. However if they obtain a mission to mine 500 <item>, the mission pay itself should compensate for the time it takes to mine that item. So those who want to basically make money doing missions would feel justified in mining 500 <item> as opposed to simply dropping into a belt and mining the hottest thing. Base value of mined materials in general would be severely reduced, and instead the player would want to fulfill a mining mission for maximum payout. That said, the mining and trading missions should be generated more plentifully based on market demand, so someone who has spent 2 hours mining blindly would still be able to turn in all the stuff they have because there are enough missions to compensate for the demand. If the player sells the items without obtaining a mission, their payout is drastically reduced in comparison. This scales the payout for the demand being more focused on the mission payout as opposed to the raw item dump. And of course, fulfilling these missions would update the demand, however if the player picks up a mission before demand is 0, and demand drops to 0, they still get paid the appropriate value based on the demand at the time of mission acceptance.
Ranking would still affect what missions the player can obtain, and the higher ranked missions would of course pay the most and require the most materials to fulfill.
Ex: A Penniless player would only be able to obtain missions with a certain cap in payout due to their rank, but if they spent a bunch of time mining and wanted to just straight sell the materials they could - but the materials themselves wouldn't be worth it to them as much as if they fulfilled a mission.
Exploration Ranking and Pay:
No longer based on credits earned. Ranking would be based mainly on mission rewards as well as the count, depth, and distance from the system entry point of planetary bodies scanned. New surveillance and exploration missions would be introduced for scanning systems (Ex: Obtain 5 complete system scans in <certain sector or location>). Possibly even introduce hostile missions where the player is required to survey a hostile system, thus increasing the chance for getting attacked. Payout for exploration missions would be very good. As for explorers who just want to fly out and explore (and basically never come back), their rank increase could still be obtained by the count and depth of the scans they do. When they get back to a station, they'd be able to sell their data as they have now, or see if there are any missions to fulfill first for the maximum payout. Let certain factions be interested in different types of systems (enemy, nearby, long range / across the galaxy) based on their state for the purposes of mission generation. A Mostly Aimless pilot would have access to smaller requirements for their missions (fully system scan 1 system within 5 LY), and an Elite pilot would have access to larger or more complex missions (Scan 20 systems nearby, Fully Detail Scan 10 systems 1k LY away, etc). Of course, this would go with the same kind of count scaling as combat (picking up 5 of the same mission type to scan 10 systems would mean the player would start at 0/50 systems scanned, and every 10 systems they'd be able to turn one in if they wanted). For a new player, that means they would have to hunt for more missions of smaller types. Just make these missions more plentiful. Mission payout needs to be reasonable though. Get rid of the 50M mission cap, especially for the missions that take literal weeks to complete. If I'm going to spend 6 days flying across the galaxy non-stop for someone, it better be worth it. Also, if I spend the time to fly out and do a full detailed surface scan on a planetary body 2M Ls out, rank and pay should increase for that as well. ALSO, for individual planet scans, let us know at the time of the scan what the base value is worth (similar to as if you had just destroyed a ship and seen what kind of base bounty it was worth).
Naturally, all subject to adjustment. But I think utilizing the mission system for primary rank increase and pay would do a lot toward balancing everything out.