We can at least try to classify the factors that have an impact on difficulty.
First, lets see what can be modified on the Phalanx' side...
Money
Enables item purchase, hiring and firing, building etc
More money simply means that the maintenance of the current status becomes easier. Also growing the organization will be easier.
Research times
Enables the use of new technology or the gathering of valuable knowledge
Shorter research times mean we can respond faster to the technological progress of aliens, enforcing our options to cope with the aliens.
Even if we have lots of money (giving us flexibility in organizational issues), longer research times will put constraints on our ability to follow alien progress. The inbalance however, could be overcome with money, since money will enable us to take certain measures, like building new bases, having more vehicles, recruiting more soldiers etc.
Restrictions on items, vehicles and soldiers
Items, vehicles and soldiers are our tools in tactical combat, the more these tools vary and the more we have of them, the higher are the chances that we succeed tactical missions, sometimes because of the simple fact that we outnumber the opponent quite heavy or because the total fire power we can employ is simply to much to resist against. Also in the long term we won't face any shortage of items, vehicles or soldiers, especially in times in which alien attack waves become more intense.
However, if we allow just two new units a week, or simply increase the price of these, or simply reduce the amount of money available, the result will be shortage, sooner or later. This will reduce options and mobility, thus creating pressure and difficulties in management and maintenance of status.
Carrier capacity
Affect the number of units that you can take with you in combat.
Could cause difficulty if combined with less money (you can't buy lots of vehicles) and bigger alien squad (you face the danger of being outnumbered in combat)
The Alien side...
AI
Alien behavior will have a direct impact on the outcome of tactical missions. Hiding, coming form behind etc...This will affect our losses, civilian casualities etc.
Alien numbers
Again having an impact on tactical mission difficulty. You simply need to fight longer and more effective to fight more aliens.
Alien weapon stats
Capacity, range, destructive power... they are quite decisive in tactical combat. A unit with a rocket launcher can be quite effective.
Ammunition
The number of ammo that an alien unit can use in total. It's more difficult to survive the attacks of an alien with a rocket launcher that carries six grenades with it compared with an alien that has just two grenades.
Alien skills
An alien with higher accuracy will be more dangerous than an alien with low accuracy.
Alien armor/protection
An alien with stronger armor will be more resistant to damage, thus more difficult to kill.
Alien TUS
An alien with more TUS, will have it easier to approach, fire and retreat.
Sophisticated alien moves or alien tech
An alien that can fly, is invisible to a certain degree etc enjoys tactical advantages in combat.
Attack intervals.
These decide the number of missions we have to fight. Thus the interval has an impact on consumption of items, hired staff and in general, expenditure. Low income will cause shortage in the long term. Adding longer research time will make the situation even worse.
Alien Infiltration
Causes change in the stance of our partners towards us. It results in lower cooperation and finally, the denial of goods and services.
Could have an impact on organizational issues, access to cruical items needed in combat... actually it can result in a lot of trouble.
Infiltration rate will be depending on attack intervals.
Both sides...
Rewards and penalties for tactical mission
They will have an impact on income from tactical missions and the reputation of the Phalanx
As there will be a limited number of missions, it is hard claim that rewards or penalties will have a very big impact. But if reputation has an impact on the weekly payment of the UN, then this can be considered as a money issue.
This topic must be also related with the Alien side, since alien performance definately will have an impact on the outcome of tactical missions, thus affecting our level of reputation in the the eyes of the UN. There is a direct correlation between alien strenght and reputation-based Phalanx-income.
Capturing items for research
New items mean new research, which means new means to cope with alien threads. Research also enables us to reproduce captured items or make use of the ones we have already captured, meaning we have lower costs, we can make some extra money by selling those items, and last but not least, it means we gain new advantages in tactical combat due to the weapon features we can make use of.
Capturing items is depends partly on alien behavior and skills, so it's basically determined by the rules and sequences of tactical combat.
This makes the topic an alien related one in first stance. But due to its impact on money issues, it must be seen also as an Phalanx side issue.
I believe this is one of the key elements in the overall game economy.
Longer research times will also have an impact on how much use we can make of captured items. Longer research means, it will take longer to benefit from the capturing. Longer production times of these items will also have an impact on the money that we can make during a certain period.
TBC (To be continued)