I have also been playing with SH Ironman (though with backup copies now and then, and I have reloaded a couple of times in early-mid game, so not true ironman); now I'm at the stage where it's no longer possible to fail and I'm preparing going to T'Leth soon. For superhuman ironman at least, by far the most difficult and annoying random thing are hunter-killers. With bad luck, even two barracudas loaded with squall missiles might fail in protecting the transport if you get bad dogfight RNG. (And you might stumble on HKs even before you get barracudas if you're unlucky.) And if the HK is targeting the transport, I think they will always succeed in killing it until you get Manta due to their superior speed. Also, if you get a shielded HK, you are toast until you get Manta or PWT launcher (you get shielded HKs at least in month 10 with 10% odds, and they are the majority of base defenders in month 14, by which time you should be able to deal with them).
Otherwise, playing with IM is more enjoyable from most points of view, because you will need to deal with occasional losses and need to be more careful. On the other hand, it also results in more defensive and slower tactics. Personally, in X-COM I like the early/mid-game stages the most because they are more challenging and RNG affects the game the most (for example, do you get manageable medium and very large ufos, which terror/special missions you get - in TWoTS this affects the most how early you'll get access to gauss, sonic and through bio-drones sonic manufacturing; the second tier of RNG is when you get armored gillman/lobster technician and heavy aquatoid or other high navigator).
I agree that sharkmen are rather tough in the phase they arrive. Especially the terror missions with bio-drones can be really terrifying - I may have aborted all of them as soon as I was able to obtain bio-drones for research purposes. Sharkmen also have excellent heat vision so you can't rely on dye grenades (which would have helped with vanilla TFTD and some other aliens). I dealt with them with GC-ZR and lots of grenades (using instant grenades makes the game run a bit smoother) and gauss sniper rifles (by shooting from far enough that they don't get vision on you). On the positive side, you don't usually have to worry about MC attacks (artifact sites do have an Oct, if I recall, though).
When playing ironman, IMHO in battlescape you can get screwed the worst by MC attacks. Especially in the stages where you are using gas cannons with explosive ammo. As soon as someone panics in the craft, (s)he is liable to shoot around and kill almost everyone and destroy your loot pile. So always when there is a danger of MC attacks you will need to have everyone drop their hand-held weapons at the end of every turn and pick them up the next turn. (Of course, there is also the same danger of someone panicking if your units die.). Luckily you'll learn rather quickly when you need to be really careful. (BTW, why gillman very large ufos have a MC-capable alien, probably the commander, not sure if that was the case in vanilla).
Some random notes on mod design, balancing etc.:
- it's rather annoying that protection from acid is gated through polyph autopsy. You'd usually want to have the extinguisher in early/mid game when deep ones and calcinites are abundant, but at that time it is very challenging and time consuming to deal with a map full of polyphs. Not sure if it would make sense to change this somehow. If not by changing the research tree, another possibility might be to decrease the number of polyphs in those missions to make them more manageable.
- shard guns are useless by the time you can learn how to use them (I didn't even bother researching them in this run). Also, not sure if humans/mutants using sonic weapons makes sense (how did they learn to do so, yet cannot tell you anything when interrogating them?). But I won't repeat what I have said before on this topic.
- most of church missions cease when you research STR_CHURCH_DATA, but for example the church still keeps attacking military bases (but has abandoned attacking shipping lanes). I'm not sure if I get the logic of this (is Interpol so inefficient in stopping the church?). Of course, I like this church "terror" mission, extremely easy in mid/late game. But I wonder if it would make more sense to replace these with, for example, the more difficult aliens vs. military missions.
- likewise, mind worm terror missions are very easy and somewhat boring when you have obtained MC protection, and they seem to be spawning rather often. I wonder if it would make sense to at least reduce the spawn rate after you have researched mind worms hatchery or some such or some other advanced tech (i.e. obtained everything you need from them).
- the abyssians keep spawning missions (and you keep shooting them down) even well past after you have obtained the treaty? By all logic all of these should cease (or actually, you shouldn't see these missions, for example alien colony expansion, anymore).
- MC-protected aquanauts appear to have bravery cap of 60, so in a few transformations a few 70 bravery aquanauts have been downgraded. I wonder if this restriction makes sense (but of course, it doesn't really matter either.)
- MC armor and MC battlearmor have built-in modules. While this causes some interesting choices as a player (you'll need to decide which guys get MC armor and which MC battlearmor), I wonder if it makes sense that you cannot produce a handheld MC controller to be used independently, or with MC battlearmor.
- there are loads of essentially useless research (but clutters up, for example, the research selection). I suppose nothing can be done about that, as removing this content is probably also not worth it. I suppose you should probably need to have 300-400 scientists if you wanted to go through all of it and not significantly delay finishing the game. (In all of my campaigns, I have had only 200-250 total, spread around 2-3 bases, but I think I should aim for a bit more than that once you get your sights on sonic and the research tree really opens up.)
- some nitpicks: the description of ION armor says sonar 10, but it's actually only 9. The description of Adv.Bionic Armor should probably also mention camo 6.
