Very few games ever actually have a point. It is meant as a distraction and as a means of being able to get small rewards in the main game such as transwarp destinations. Basically it is STO's version of Farmville when combined with starbases.
There are some nice things in the game which you can only acquire from the Duty Officer missions. Sure the rewards from each individual mission are small. But, do them for long enough, and then a few more, and then a few more, and you wind up with a lot of sellable swag for minimal effort.
I don't really see the point in most doff missions besides marauding and fabricate prototype console missions. The others require way too much micromanagement for to little reward. I pretty much ignore the doff system now besides for making occasional marauding contraband runs, I'd rather just get straight to shooting stuff rather then click on missions the player can't even participate in himself.
If you don't do doff missions you can make a lot of money just by running recruitment missions and selling all the doffs, although with the new dil costs for recruiting it remains to be seen how profitable doing this will be.
Anyway don't feel compelled to do this doff thing just because you se most people doing it, I've ignored it for months now and still have all the items and money I want, it doesn't hold your game progression back in anyway aside from missing out on a few titles, accolades, and minor perks like a uniform, transwarp, and more doffs you don't need.
Individual doff missions don't give much, as you stated. But making one's way to the higher commendation tiers, gradually getting better doffs, and of course a few EC here, a few contraband there, can greatly improve a player's income. Especially since the opportunity cost for doffing is relatively low: the doffs are not consumed, and setting up the mission is as easy as a few clicks, so with proper planning the time input is marginal.
The elegance of the doff system is that it offers players great discretionary control over their progression. Do you just want cold, hard EC, right now? Do you want to farm CXP to plow into fleet marks? Do you want doffs to sell for more EC? Dil? Or do you just want to collect rare doffs? The doff system lets you pick the priorities that are important to you.
Doffing can be undertaken intensely, as you noted, or it can be done incidentally, during downtime, or while flying from mission to mission. The flexibility and incidental practice of doffing makes the game more fun and reduces tedium, and makes your time usage in-game generally more efficient.
From your post, OP, I gather that you are just starting out. Doffing is investment, and like all good investments, it has a real snowball effect. The first few missions don't seem very promising, but as you gradually get green and blue doffs, the completion and crit chance for most missions begins to rise, you'll get more satisfying rewards. It takes patience and planning.
I recommend nabbing any budget doffs you see. Poach underlisted doffs on the exchange. Pick up world event doffs, or any of the so-called "ultra-rare" doffs that come from the glutted lockbox reward packs.
the seven purple "ultra-rare" Gamma doffs (especially Saro Shonin and Paulapo)
the four purple and eight blue Temporal Agent doffs (especially Isis and Juel Ducane)
the blue quality photonic Shakespeare doffs (purples are usually uneconomical)
do the "Facility 4028" Cardassian War episode for the doff pack reward
Geologists, Advisors, Biologists, Biochemists, Armory Officers and Transporter Officers
Remember, you can have duplicates. Your early roster will probably be pretty homogenous, with many dupes of cheap doffs. In general, blue-quality doffs will give you the most bang for your buck early-on, until you outgrow them. Blues are relatively cheap; buy as many as you can, especially Vulcans. Because of their bad traits, early doffing is MUCH slower as KDF.
A well-spent investment of about four million EC (the yield from two Explore the Galaxy events) will go a long way getting you started on doffing (enough to buy about two dozen blue doffs), and with good planning, you will make it back in short order, especially since you can resell the initial doffs.
turn in contraband = 2k dilithium every 4 hours. If you can't gather contraband via the doff system then you can purchase 5 for about 200K EC on the exchange. Don't have 200 EC, then farm a couple of recruitment Doff missions for refugees from the colonies and sell them on the exchange for anywhere from 90k-200k. The Doff system is really a good way to line your pockets in either Dilithium or EC. Also once you hit lvl 110K in the doff system in a certain field you can sell off 10k Doff points in each category for fleet marks.
So yes it is a useful way to move ahead in the game.
It's a mini-game or a game within a game. You do not have to play it at all if you do not want. Granted, the Diplomacy commendation will grant Transwarp ability to specific loctions, a nifty jacket for your Captain, and a neat sector travel buff.