What I will write now will probably cause some rage, but please don't just reply like:"Your idea is bad, and you should feel bad".
First of all, there should be two kinds of resources, resource A and resource B.
Resource A will have a steady income from the areas you control, while resource B is obtained the same amount per faction(i.e. Orks would have as much as Space Marines, Chaos and Eldar). Resource B would be paid out to the WC and then distributed to the SF manually, while resource A would be (a previously set amount) distributed to the SF and then manually to the Squads, and the rest would be paid out if needed(i.e. there's a lack of tanks at Base C, so let's give the SF there 500 resource A).

Resource A will then be used to spawn vehicles, heavy infantry or certain kinds of weapons, which shouldn't be spammed(same way as in Planetside). Resource B would then be used by the SF leaders to award certain squads which fought amazing at a certain battle. The Squad Leader will then award certain players for their experience and performance by unlocking them weapons/ vehicles/ loadouts/ whatever. This would mean if someone is really good at aiming, he would get a sniper rifle, if he's good at driving tanks, he might get the allowance to drive MBTs and so on and so on. This would allow for a good specialization in between squads, because the Squad Leader would always know what his soldiers have got. Of course should people not be assigned a certain squad and stay in there for the rest of their lifes, but should be able to be transferred to another squad.
Resource A would be obtained from certain bases like mines, research labs, manufactoriums etc. The enemy could just cut off your supply by capturing said bases, so you have to watch your rear, otherwise you WILL run out of heavy stuff.

Trophies should be awarded in the same way. The WC decides a certain battle which has been really good, and then award the SFs which has been around there. The WC can then decide if they want to award everyone who fought there with something like "Veteran of Battle 153", "Breacher of Base XYZ" etc. These awards can only be given out 1-3 times per month. Apart from that, they can also decide to award only certain players. Then would the SF leader decide which squad fought best, and then the Squad Leader would again decide upon one or two players who made the highest effort.
These trophies would be only ribbons, purity seals and stuff like that. Another kind of trophies would be something that you individually tear(literally) of your enemy, e.g. their heads, teeth, armor parts, to show off that you killed an enemies champion.

So yeah, Champions. From time to time some kind of "Relic" should be discovered under the battlefield. You would have to capture the territory and hold it for, let's say, 3 days for a mining team to drill down to it. Afterwards, an incredible hard dungeons would pop up, requiring the best soldiers of various SFs to take part in it. Once it has been cleared, the Relic would be discovered and immediatelly transferred to the WC. They should then reward someone in the same way as mentioned above. Due to them being so extremely rare, only the most experienced Veterans could get them(basically, everyone could get them, but who would give such an awesome weapon to a noob?). Unfortunately, these Relics are also the reason for the Tyranid activity on this world. Once they are discovered, that means indicated on the map, but the dungeons isn't cleared, the Tyranid will start attacking said base, getting stronger and stronger with every attack. This would prevent people from just sitting on that Relic, not being able to clear the dungeon, but also not letting lose of the base.
These Relics would be unique, named, extremely cool looking and better than usual gear(they would give you the advantage in an otherwise fair 1v1, or even a 2v1. Skilled players, e.g. other champions, or just 10 random people teaming up, would be able to bring that champion down though) and of course be shown off in the SF strike cruiser's trophy room, whilst not on the battlefield.

EDIT: Epic wall of text, lol

Add some break returns between paragraphs would help some of that wall not feel so massive.

I like the idea but I think it would be kinda hard to implement just because it requires so many players to "hand out" the resources. I think they should be automatically allocated based on the players location and the state of the supply lines in their location.

For example a territory close to the factions fortress would have great supply lines and thus more of the factions resources would be available to spend there. Where as the outlying territories would have less stable supply lines due to attack and distance from the HQ resulting in less resources to spend at smaller out posts.

I do like the idea of the WC handing out trophies though. That would keep people from just grinding to get a shiny trophy and it would encourage them to play the game and work as a team.

I agree on the point that it will really hard to implement it though. But if it WOULD work, it would be simply amazing.

Its already known that players in higher ranks allocate rewards.

Handing out rewards would be ok, things like trophies and badges and such, but actual resources to buy tanks and other things might be kinda hard to organize.

This would be the exact reason for a certain amount (60-80%) bein automatically distributed

Maybe instead of passing down the resources from the WC the SF/Squads could earn extra resources from completing objectives given to them by the WC. That way the WC wouldn't have to manually hand out credits and they could spend more time managing the forces and less time sending out credits.

In M.A.G on the PS3 in the 125v125 battles, generals and squad leaders would give special orders. It could be something stupid like "go destroy that one jeep at the other side of the battlefield" BUT you would gain extra xp if you completed it. Imo it's a cool way to have the players respect the chain'o'command.

That is one of the things that scare me the most.
Having suffered from that recently in GW2 (unable to defeat a world boss because you loose 90% of the right flank running after one sub-boss to get loot that 98% of the time is crap) that is an issue I am really concerned about.

Hordes of lol-players running after a carnifex in the middle of the battle because "yolo xp and loot" would be terrible

That seems like the ticket. Squads/SF get requisition for completing objectives - perhaps more for doing the "assigned" objectives than just free-wheeling. Perhaps certain objectives and strategic points taken would offer more requisition - like a resource node (manufactorum) offering more than say a firebase or fortress. Plus, holding a manufactorum would offer requisition over time when you're holding it.

I'd say the only people that can use the requisition for anything more than personal weapon/armor/gear would be the squad leader and second in command (if there is such a management mechanic in-game). So only a leader of sorts could requisition a vehicle, and anyone in the squad can drive it. For more organized groups, the person driving it would be assigned (probably the best for the job), for less organized ones, it would be the first person to jump in it... and get it blown up.