Remember, none of Morocco's uniques are disadvantageous: even if they don't really add to the civ, they don't take anything away. Even if gold and culture from trade routes is pointless, it doesn't make any trade routes worse than usual. Even if Kasbahs are pointless to build, they don't stop your from building the improvements you actually want to build on your tiles (eg. farms). Even if their cavalry UU's bonuses are kind of pointless, you do not have to build cavalry UU's and even if you do, none of those bonuses can ever be bad for you (it'll be like having a non-UU cavalry as opposed to a worse cavalry).
India: go tall like you're supposed to.
The problem isn't just the fact that they cannot go wide, it's that plopping down a new city gives 7 unhappiness instead of 4, making early expansion to those 3-4 Tradition cities even more difficult. The effect diminishes in the long run, but it's still a disadvantage. The fact that you have slower Chariot Archers also means that Chariot Archer rushes are a lot more difficult for India.
Byzantium: don't use dromons for conquest and/or never build them
Dromons are actually great for conquest because they're essentially like Chariot Archers of the sea, it's just that you cannot use them for conquest alone, you'll need to at least bring a land capture unit along somehow (or just use Dromons as a support unit for your land force). It's really only a disadvantage on island maps in Medieval Era, since your opponents can use Galleases with a Trireme capture unit while you have to awkwardly bring an embarked land capture unit along.
Another possible disadvantage is that their Horseman UU has less movement, worsening its ability to act as a capture unit, but being able to receive defensive bonuses essentially turns it into a blocker, so the fact that it is a worse capture unit becomes sort of irrelevant.
Iroq: the longhouse is better than a workshop until a cutoff point around the industrial era
This isn't necessarily true: the cutoff point depends on the number of worked forests you have around the city. Since other civs can chop those forests for hammers but you cannot because you're relying on them to eventually make up the production difference between the Longhouse and the Workshop, there not only is a cutoff point to Longhouses, but you also cannot make use of flat production from chopped forests. This is the sole reason a few civ tier lists place Iroquois among the worst civs in the game.
Venice: they're the crappiest civ because of their gimmicky UA anyway
They're not crappy because their UA is gimmicky, they're crappy because their uniques are not well thought-out. Austria's and Spain's UAs are gimmicky too, but that doesn't make them crappy. I've got a few ways that their uniques can be changed to actually make them viable (more control over puppets, swap Great Galleas for a Monument replacement UB that lets you generate GM's early, free GM from Optics changed to free GM in Classical Era, map spawns extra CS if Venice is in the game, Venice's start location is treated as if it were a CS to let it spawn near groups of CS's), but that's for another thread.
I also thought of a few more disadvantageous uniques:
- Spain's knight UU costs 15 more for the same combat strength. Sure, it's to offset how you can found cities on other continents with it, but if you never use that ability, you're basically getting a Mandekalu Cavalry (no city attack penalty, embarkation defense matches Songhai's UA) that costs 25 more , and the increased cost arguably makes the UU worse than knights.
- Inca's UU retreats from attacks, so they cannot be used to guard a civilian units, removing one of the most useful abilities of archers.
- Shoshone Pathfinders cost 20 more than scouts. Granted, they're pretty incredible, but the increased does mean that Shoshone can't build additional scouting units as quickly as other civs, and when that's all you're looking for and don't need either the extra strength or the ruins choosing ability, Pathfinders are worse than Scouts.
- Hun's Battering Rams cost 19 more , can only attack cities, have 3 lower effective combat strength on defense, and do not receive defensive bonuses from terrain. This means that if you're looking to use spearmen as regular combat units, Battering Rams are strictly worse than spearmen... though you're doing something wrong if you're looking to use Battering Rams as spearmen replacements rather than better, melee catapults. Still, I thought I should mention this, for completeness' sake.
- Korea's Hwach'as have 16 less effective combat strength when attacking cities than Trebuchets. Granted, neither is actually that good at attacking cities, and Hwacha's are better at pretty much everything else, but I thought I'd mention this for completeness' sake.
- Korea's caravel UU cannot be used for scouting or capturing cities across oceans like a regular Caravel. Like the Dromon though, the UU's combat strength is so huge that it's effectively a different role entirely, so the disadvantage has more to do with not having a Caravel instead of Turtle Ships being worse than Caravels.
- Siam's knight UU has 1 less movement speed than knights. Granted, their other bonuses more than make up for it, but if you really need that knight movement speed, you won't get it when playing Siam.