I am with you on making everything avilable. Just need a way to limit things from bleeding over too much when combining. You want that stuff to be exciting and cool but we have all seen when two things collide unforseen effects can ruin gameplay.
I assume you read up on my points system with limiting Offense, Defense, support and utility. Let me elaborate more on it.
If we throw in passive boosts (like perks from FF), primary and secondary weapons into the point system and let those passives and weapons also cost points then it could be balanced easily. Give a player 10 slots and let him fill it up with as many weapons, passive and abilities as he likes as long as he stays within the 4 limits being "Offense", "Defense", "support" and "utility". Lets call them the 4 attributes. passives cost the least, weapons cost somewhat more and abilities the most. If you want to play as an Ember magician then you can will everything up with abilities but you'll have exhausted all your points by your fifth ability and won't have any weapons or passives. You can go fully loaded with guns but guns are kind of heavy and you'll miss out on those sweet abilities and passive boosts. If you want you can go full passive with melee only. Whatever flouts your boat.
From the start every players has 100 points in each attribute he can spend on abilities, passives and weaponry. The way you specialize in one of the attributes is by equipping gear such as motors, armor plating, pistons, thrusters,etc. that increase one attribute at the cost of decreasing the other. Heavier equipment give slightly more points but increase your hitbox size and make you slower.
limiting it with "mass", "energy" and "CPU" (like some suggested from FF) is to me arbitrary but if you limit at the root of the problem by directly limiting the attributes you make it impossible to attain the holy trinity.
some clarification:
Offense: Raw damage output, damage enhancers, elemental mods.
Defense: armor increases, shields, invulnerability, elemental resistances, damage negations.
support: buffing other players, healing other players, enhancing stats of other players, anything that interacts with other players, AOE, crouwdcontroll, stun, aggro-takers.
utility: self help like movement enhancers, non damage dealing deployables, barriers, self support, self heal.
if an ability, belongs in multiple categories then it'll cost points in all those categories. Some examples from FF would be:
Afterburner: heavy utility.
heavy turret: Offense and support
trailblazer: Support and utility
thunderdome: Defense, support and utility
Fusioncanon: Offense and support
Necrotic Bite perk: Offense
Invigorate perk: Offense and support.
Explosive Rounds: Offense and support(because of AOE)
Health Surge perk: utility
Now all we have to do is add perks and weapons to the progression tree and we're set. ^_^
(my advice, don't copy over FF abilities, perks or weapons, they are crappy and unbalanced, better start making your own unlique stuff like FF never existed)
Here is an example of how I image the Ember progression tree to look like. It's a teck-tree from "Sid Meier's Civilization: Beyond Earth"