Admittedly I've not played a full Cultist game at this point, but I played for around 30h with different races and faced them and I don't really believe what you're writing here.
Faced against
who? The AI which we have established already is pretty inept, or another player playing as the Cultist? That makes all the difference, really. The AI isn't smart enough to use the unique flavors of all the factions.
Seems to me that for the Cultists to work their opposition has to be extremely passive in both expansion and warfare, otherwise it's piss easy to cripple (through village raiding) and envelop them.
Your enemies can't just expand like crazy right off the bat, there is happiness to consider and loss of unhappy cities lead to decline in food and industry production. Having more cities is worthless when they are all too unhappy to progress with anything. By the time enemies can start expanding further than the initial 2-3 regions you should be able to counter them and be able to go and raze their new settlements. It should be early enough for the minor village units to still be enough of a threat so you can start harassing the enemy with them.
There's only one faction who can expand like no tomorrow without a care for happiness and it's the Broken Lords, but that's ok. The different factions are meant to one up each other.
I'm not that sure about the availability of the resources either, what with the market prices and AIs general unwillingness to cooperate
Now I'm not even sure if we are playing the same game anymore. Market prices are what they are, they get exponentially more expensive but you get exponentially more money as well. It's not a final solution, but it is a very important and strategic tool to use. I've never found the AI to be unwilling, though. In fact I find it all too easy to exploit. You steal / sack a few of their cities, wait a few turns and then offer peace while demanding all their strategic resource. It never fails. The AI is less likely to give you any tech unless you are willing to trade something yourself, but they will give you stacks of 300 glassteel like it's candy.
I had no problems with keeping boosters up all the time with big empire the bonuses they give is just crazy +50% production/science/food/constant top happiness for all your cities lol wtf gg, Vaulters' strategic boosters are just added overkill.
I usually have no problems either, at the mid-end game when I've conquered more than half the provinces. Cultists can do it from Turn 1 without stopping at any point. Therein lies the difference.
And what's so bad about Vaulter units? They start with ranged, best option, while Cult starts with support, worst option by far, especially considering that you probably want to make your hero a governor in order to not fall behind expanding opponents almost immediately.
Marines aren't the best option by virtue of being ranged. Here's a unit breakdown:
Marines have 68 HP, 47 Attack, 31 Defence, 21 Initiative and do 34 Damage.
Wild Walker Dekari Ranger's have 60 HP, 58 Attack, 19 Defence, 38 Initiative and do 32 damage.
The Dekari Rangers simply blow the Marines out of the water as far as ranged units go. The only stats that really matter in the early game are Initiative and Attack, which the Vaulters suck at. Their low health and low initiative means that pretty much every single unit is going to move before they do, and they are going to squish them easily like bugs. Low Attack means that at higher difficulties you are going to be doing 0 damage per attack quite often, which is the infuriating way to a swift end.
Now why didn't I compare Vaulters to Cultists you may ask? Well, one reason is to show you that Vaulter Marines are early on very shit, but also simply because there is no question that Cultist units are horrible as well, which is why
you aren't meant to go fighting around with them. There's a very specific reason why the Cultists begin with the Bribe and Parley tech and the reason is that you use those tools early on instead of trying to fight everyone.
Actually the most dangerous weapon in their arsenal seems to be the fact that they instaraze cities on successful assault, this can really hurt your opponents if you manage to rush them. But later on I don't see them having a chance against a player of similar skill, especially since the unupgraded village units are any good in second era tops, later on just pointless cannon fodder.
It is a very useful ability to instaraze towns. You don't need to worry about defending bigger important cities and not letting the enemy to retake them back. They simply lose everything and every loss for them is a gain for the Cultist.
As for village units, keep in mind that each era gives your units a +1 to their initial level when produced, this also affects minors. It also makes them more valuable each era which means that you will get more and more money for selling them. The techs that unlock more garrisson space affects the minor villages as well!
Give the Cultists a try, brah. You know you'll love them.