HotspotsThen have the hotspots repeatedly change, preferably along the path to the mission objectives.
DTsSay DTs are one shottable. Suddenly, Spider Mines and Firebats have more use due to splash; you wouldn't even need Comstat.
BunkersI'd like to note that Bunkers are useless due to the lack of armor upgrades for it. You could have it at a lower HP with 255 armor and a slow repair speed so it's viable even later game.
ProtossA simple fix could be increasing the max number of summons AND making Protoss summons free.
Gameplay ItselfRight now, the main hero character (Kerrigan) is literally invincible until the last cleanup mission (zombies gain vision of you) if you pop the energy ability. Combine that with easy farming hotspots and the optimal strategy is to get the best farmer (GHOSTS) to the best hotspot ASAP while Kerrigan runs around between mission objectives.
You are rewarding only one playstyle; farming. This is why the Ghost is so damn powerful. It is extremely upgrade efficient (lvl 3 can kill 100 hp units, lvl 9 or so can kill 150 hp units) and summonable, which allows you to spend resources on cheaper troops instead of rising upgrade costs. It has ridiculous range while having a small size (fits more in an area) and decent firing speed (not penalized for overfire the way Metal/Protoss is). It can make it up the most important ramps for farming purposes that Metal cannot. Furthermore, there is no need to monitor your Ghosts; once they're in position you're golden.
There is no one better at farming. Number two would probably be Marine+Medic+Firebat simply because they require less attention; you just have to make sure your Medics have energy. Their fast fire rate is also very forgiving in not wasting shots.
In comparison, Metal requires continuous monitoring for repair. Despite their range, they cannot make it up the ramps to the good farming spots. Their slow firing speed means that despite 1 hitting everything, the enemy can still close in, especially if 2+ units decide to fire at the same Zombie.
Protoss...ugh. More units wouldn't really help the cause because there is no means of healing them. You could possibly make Protoss units free to compensate, but even then you would need a constant vigil to constantly create new units. That and the speed of the attacks (both weapon sprites take time to come out) practically guarantees that they will get hit.
Balancing it might be possible, but it doesn't change how the general gameplay is to farm with troops while invinci-Kerrigan roams the map. I think the core issue is that different choices do not allow for unique styles of play. There is no set theme for character archetypes. Why must I always have a Kerrigan hero? What about a DA hero? Or a Probe hero? Why must I be limited to the same summons despite my class?
What if I wanted a sneaky playstyle? Let my main be a cloakable unit like Infested Duran with a focus on the Spider Mine ability, perhaps with a Hallucination Summon for distraction, with uber high damage and low HP. Have an Infested Terran summon for both damage and for consume. Have him be a disabled sprite so that Zombies can pass through him. Have enemy detection units that I have to kill (slow moving overlords perhaps).
What if I wanted a summoner playstyle? Let me be a Medic with an ability to control nearby Zombies, but have a limit to the max number. Set Infested Kerrigan Energy to 0%. Give him a heal all allies ability and/or a restore energy for the Medic as well.
What if I wanted a spellcaster playstyle? Let me be a Dark Archon who can Maelstrom (no MC). Let me summon High Templars with Storm (no hallucination). Give me an ability to reduce enemy HP to a low %, and/or maybe a Defiler summon with Plague. Or maybe even Science vessels with Irradiate.
What if I wanted a tanking playstyle? Let me be a SCV who can summon a Metal ground unit that starts at 1% HP, a super high max HP, and a slow repair speed. Give me a summon for a Metal ground unit with decent damage and lower HP. Add in Science Vessels with Defense Matrix through the Shuttle.
What if I wanted a ranged playstyle? Let me be a ranged unit, your choice which. Give me two or so summon types with different upgrades to force me to balance upgrades based on my style. For example, I could get Marine summons and Siege Tank summons.
The above are all really simple abilities off the top of my head and not well fleshed out. You could also have timed invincible units. If you're fancy, DDS and AI scripts (Irradiated Scourges) could make even more interesting abilities. Nonetheless, it should get the idea that I'm emphasizing across.
Use different character themes and reward different playstyles. Since the only cloakable hero is owned by the Sneaky themed class, farming has be balanced against assaulting the mission objective locations. The Sneaky class won't be that simple as he has to deal with detection as well. Take a look at AoS games for more theme based ideas; the PvP ideas can't be used, but there are plenty PvM concepts that are viable.
I can understand if you would prefer to balance out the existing gameplay for simplicity's sake. However, I believe that your gameplay is inherently flawed and biased such that only one playstyle is truly viable. I'd recommend rethinking your game and adding more playstyle options.
None.