Actually, what it does is kills versatility in a role designed for diversity.

I did some thinking on the logistics bonuses and like I mentioned earlier in the topic, the need to be more generalized while being equipment oriented instead of tied down to a single piece of equipment that you're not always going to carry given the circumstances you need to adapt to in a single battle. Also, we're going to get more equipment at some point and for a class meant to use equipment, shouldn't their bonuses affect as much of it as possible?

Gallente: +5% to equipment range per level. Instead of being tied to one thing, you get a bonus that can affect the effective range of nanohives, reppers, the active scanner, the blast radius for REs/Mines and can fit with other equipment we might get later like target painters, bubble shields, webifiers... etc.

Amarr: +5% to armor repair module efficacy per level. Honestly, there's really nothing wrong with the Amarr bonus. It fits with the suit as an assault/logi hybrid and since it affects armor repair on a suit that only gets 4 low slots at prototype it's not overpowering. The only change I would make is to extend that bonus to reactive plates as well to add more flexability to the suit's armor tanking options.

Caldari: -5% to equipment cooldown per level. Similar to the Gallete, this would affect a broader range of equipment instead of one thing, but just like the Gallente, focus on reusable equipment. This would apply to the active scanner, but later down the road any and all equipment that would have a cooldown like anything EWAR related.

Before I go into the Minmatar bonus, I still don't see what the issue is for a suit bonus that only works in 2/3 of the game's available modes. I'd rather keep the hacking bonus since it's what everyone wants logistics to be- non combat oriented. But if the bonus has to go, I'd suggest something like this.

Minmatar: +5% to deployed equipment carried per level. At max level this would affect how many nanohives, uplinks, and later on bubble shields, proximity scanners, decoys, or any other deployed equipment that would come into the game.

There is a problem most of you are willfully ignoring on the subject of Logis. They are not designed to be equipment mules, they just happen to be thrust into that role via bad foresight. If anything, Scouts are better suited to use Equipment. Logistics just make a good equipment mule due to their high number of slots and high fitting, similar to what makes them as good at killing as Assaults. These bonuses are meant to cinch up each suit's roles and to give each class of suits the roles they were envisioned to have.

Imagine that the game is TF2 for a moment.
Logi is Medic, but can also equip Engineer's wrench and build stuff. Due to Medic's greater speed, HP, and regen, people will always choose Medic over Engie. There is also the fact that in this little universe, Engie does not exist, so they feel that choosing Medic to Engineer is normal.

That is the state of DUST. there is no Engineer role suit, so the Logistics suit is filling in for it. When they get around to fixing the role bonus problems, they will make the Logistics suits actually focus on Logistics, which is EVE slang for Healing. They will then make a new suit for the other Equipment, like the some of the Type-2 suits used to be.

Therefore, I feel that we should make a new class of suits in the OP. The Engineer class.

Minmatar will get bonuses to Remote Explosives due to their speed and lower, but not lowest, scan profile. This may cover all the explosives, like proximity.
Amarr will get bonuses to the Drop Uplink, as they are the slower and tankier ones they will be the ones most familiar with advantageous terrain.
Gallente would hopefully get drones. Sentry drones for point defense, small drones for personal mobile support, etc. Or, they can get the Active Scanner and Point Defense Drones while GalLogi gets bonuses to repair drones.
Caldari, I'm honestly not too sure on. I'm not a major Caldari in any verse, but maybe... Webbifiers? interdiction bubbles? EWAR? Should another suit entirely be EWAR? Help me out here.

EDIT: Make shield repper. Give CalLogi bonus to Shield Repper. Give CalEngie bonus to Nanohives. Boom.

Did you consider a bonus to Assault Damage with light weapons?

I know it sounds pretty silly but I always thought of the assault suit like the wasp while the logi was the bee.

Wasps by common stero type and thin and lithe, they dart about with a painful sting, which they can use again and again and again.

Bee's/ Bumble Bees are the slower, more clumsy, by more formidable in stature, sting once, but fulfil a supporting role in the hive.

I just imagined the Assault would have high DPS, but low EHP and require logi support to stay alive, coupling that with their relative speed over the other suits, while Logis would be higher EHP, but low a DPS, harder to kill but more resilient in a fight

I'm open to ideas as long as they fit with the logi's focus on equipment. I do like where you're going with this, but there are some issues with what you propose.
The cooldown reduction bonus would be only useful for active scanner until other equipment with cooldown comes, and we don't even know if EWAR stuff will be deployable or cooldown based. I don't want a bonus based on the assumption of how a future piece of equipment might work.
5% (25% max) units carried bonus would be useless to many deployable equipment, since 25% of the maximum carried for many is still less than one. Though I suppose anything 0.5 or higher can be rounded up to to 1. EDIT: Nevermind, I see you said elsewhere that it should round up.
The Amarr logi bonus I'm fine with your idea or my idea.

EDIT: Regarding the current Minmatar logi bonus, its not so much that its an issue, its just that it doesn't really fit with the logi's emphasis on equipment, and it would work MUCH better on the Minmatar scout. The current scout's melee damage even with maxed out melee bonus is still weak compared to a medium frame's melee, and a bonus to another race's knives doesn't make sense; even if its changed to a bonus for the Minmatar knives when they come out, it will still be weird that only one race's suit gets a bonus to their knives. The fastest scout having the hacking speed bonus would make the most sense to me.

If these changes come, there would have to be an SP refund, so you could rethink your role and specializations if you need to.

I originally had assault bonus be a a 2% damage bonus per level, but eventually changed it and gave damage bonus to Gallente instead since their weapons are about DPS, and made it 5% total since many thought 10% was too much.
I suppose the damage bonus could be the general bonus, and Gallente could keep the current PG/CPU bonus but make it specifically for plasma weapons. I had a skype conversation with some other posters, and they preferred something more... interesting then the PG/CPU thing for Gallente assault.

I might change it again.

I'm about to change the proposal, I need ideas.
I can't use the max units carried for deployables thing since even if I round up, It will still be useless at early levels.
The range Idea is great (Repair tool range, active scanner range, active scanner range, nanohive supply radius).
I'm also thinking of an efficacy bonus (effects repair rate of repair tool, nanohive resupply rate, active scanner precision, RE/PM, RE max spawns)
I need a third idea.

OPENED TO SUGGESTIONS

Maybe change the skill to speed increase for equipment. Hives would pulse faster(same amount of clusters with the same amount of ammo replenished but simply faster), uplinks would spawn quicker, scan rate would be quicker but time showing would remain the same. There is an overlap with the repair tool and the efficacy option(efficacy repairs more, but this one repairs more often - should equal out to be the same amount repaired over the same time period). Perhaps this could be used in conjunction with cool downs but it may not be necessary.

It's basically overclocking your equipment.

Gallente assault would only have 5% more damage than other assaults. Other assaults get things like bigger magazines, less heat buildup (higher damage potential for laser rifle), and more range (remember how big an advantage sharpshooter was in Chromosome?).

I don't like damage for commandos, seems to assault-y