After playing the game through several times and spending at least 10 hours in the free play mode, I have come to a few suggestions being an ant nerd and a computer programmer.

Your food system is bad when ants were faced with the problem of storing food long-term, they evolved replete ants, and your system would be better if it incorporated them. no ant species would leave raw animal carcasses in their nest, because it would be certain death. Moving to repleteís would add tactical elements to your gameplay. Replete ants tiles could be killed in nest invasions.  Losing a partial amount of food if not all the food contained within.  Providing interesting level design possibilities  If performance is an issue they could remain as a tile since replete ants are completely immobile even in nature. A talented level designer could definitely take advantage of this.

My 2nd suggestion would be to move to an upkeep system based on the number of ants, and Brood in your nest. In my opinion, this would give the game a lot more depth, forcing the player to plan ahead. Scrap the replacement cost and transition into an upkeep cost, {5 food per soldier, 3 per worker,  1 per brood* } that Drains out of your food stores every 24 hours based on the day-night cycle. if your colony, does not have enough food, then your ants slowly lose health and the Queen refuses to create new eggs.  This system would be superior because it would add some depth to the gameplay that seems to be lacking.  If you implemented this change.  You could design a survival level based on feast and famine cycles,  where the player is presented with a feast day where food is plentiful, but the attacks are vicious and the point is to collect as much food and get it into your stores before the famine starts, followed by a prolonged period without access to food or extreme risk when attempting to access food. Attacks are from rival colonies or the water line comes up and blocks your access to food.  (Numbers are just examples, obviously, balance adjustments will have to be madeÖ.)

my 3rd suggestion would be to add some transparency and balance changes, to the upgrade system.  While I like the system in principle there seem to be some glaring oversights, upgrading the movement tiles only seems to allow you to upgrade the tiles around it, which donít get me wrong is useful.  However, it would be great if it had some strategic purposes as well.  For example, they could speed up ants that walk on it while slowing down other creatures.  In addition to that, there seems to be no way of telling exactly what is upgraded when upgrading a tile how much food storage is gained when you upgrade?  Is it displayed anywhere in the game?  If not,  it should be.

My last issue is Queen movement, I know the development team has rejected this out of hand, stating level design issues, but I think it is something that needs to be addressed, to add some complexity to the gameplay, I admit that with the current state of the game, adding Queen movement would make level design more difficult.  However, if the game is going to have any sort of depth long-term, this issue needs to be looked at for future updates.  I definitely get really annoyed with the fact that my Queen is in the middle of my nest, and I canít move her or remove  the multipurpose food-storage/worker tiles around her.

The colony upkeep would a good idea. But I think it should start 1 in-game day after you go to the surface.

Great ideas. I agree about the colony upkeep and therefore getting rid of egg hatching costs.
Posted from my Zombie bunker in northeast Ohio.

The idea of colony upkeep seems to be liked by many people, but perhaps there are other ways of 'feast and famine' to take place without having to change the gameplay substantially.

Perhaps there would be insects which its food carcass cannot be collect, whether it be because it has too little to offer, or it secretes an unpleasant toxin of sorts that makes it's flesh poisonous to eat.

Perhaps there will be many types of insects that work like that, aggressive, little to no payoff to kill them, and perhaps even do bad for the colony if killed (like if the insides of the dead bombardier beetle react together while still inside the body).

So far, the only insects(I think) that don't give food when killed are ants, but I think that will be subject to change.

Indeed, an upkeep system would provide essential depth to the game.

In the long run imho it will be necessary to split menus into "casual" and "in depth" in order to obtain new and all sorts of players as well as getting and keeping veterans/ant enthusiasts.

Casual would consist of all the "gamey" stuff like arena and hordes of bugs entering the players nest etc. whilst in depth would provide a more realistic angle with players having to manage the colony (including food resources, maintenance of breed, tunnels, humidity, relocation of queen etc.) as well as fighting realistic intruders and other realistic ant species (i.e. no combinations of species).

The difficulty level might also depend on which kind of species the player chooses on what kind of map given that some species are more into fighting, others more into speed needing less resources.

I have addressed queen movement in a post before, but I didn't think about balancing. I agree with almost everything, except for the mixing ants, but that is only if you were talking about other ant species, not formica ereptor.
Ants are beautiful,
but if fooled around with,
can be deadly.

Speed tiles should boost ant speed more when upgraded, and this seems to be true so far (I don't know that anyone has truly tested them). 

Food tiles: 

Lvl 1: 10
Lvl 2: 40 (+30)
Lvl 3: 100 (+60)
And on the sixth day, God created ant in his own image, and gave them dominion over the earth and all of its creatures.  Amen.

Perhaps the bugs themselves would need food to survive, and even growing to the next level of life if they survive. The level 2.1 talks about dis placing predators, but maybe one or more species actually need to be present to repopulate. Therefore, dis placing them forever or for a long period of time.
Ants are beautiful,
but if fooled around with,
can be deadly.

Perhaps, but that might also be too easy.  I'm more in support of the idea of lowering the amount of food you get from everything you kill. 
And on the sixth day, God created ant in his own image, and gave them dominion over the earth and all of its creatures.  Amen.