I say, if you need them to tell the story, use them. A lot of these "annoying" enemy groups have great story potential.
What you could do, to cut down on the annoyance factor, is make a few custom knives critters, without the caltrops, and mix them in.
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A Knives-centric arc probably wouldn't even get a full play from me, but if they show up in a mission or two, that's no biggie. If it "feels" too hard, then set the map so that it's as easy as possible or add an ally with Kinetics to Speed Boost you out of all the caltrops or something.
Allies with the caltops fields is problematic. The second mish involves some longbow to help out, but the caltrops drives them nuts and they run away for half the fights.
I could probably make due with custom critters, Knives would only technically need 3 since they only have one of each level. (minion, liu, boss) Custom critters take up way way too much room in general, though. My outcasts arc used to have a full crew (5 minions, 5 liuts, 3 bosses, 1 av) but I had to cut out 4 of those just to fit in actual story text >.>
IMO, there's so much good content in the MA that I won't run an arc with Knives in it - the story may be great, but they're an exercise in frustration, and I'd rather spend my time enjoying MA.
Of course, I only play MA solo with melee toons, so the caltrops tend to be ridiculously painful for me.
I don't mind a few spawns of KoA appearing but I would drop an arc if it turned out to be all KoA, all the time.
If only the caltrops would despawn when the caster was defeated, the Knives wouldn't be nearly so bad.
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So would this make Chimera Ninjas a no no too since they also use Caltrips?
I made a custom group that mixes Knives and Malta. Very fun, for me. I am sure some would find it painful and tedious. After all, if a defender gets stunned, that is fine, but when a scrapper gets slowed down, worst thing ever! 
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Personally I find caltrops no problem. I also almost never play melee characters so there you go 
Switched them to a custom faction which still fits the story. Could be a lot more difficult than Knives, except no caltrops
I happen to like the Knives (for me their coolness outweighs any other factor) but I understand how others feel about them.
I suggest that if they are going to be the centerpiece of a mission that you (if you can without messing up the story) break up the map full of Knives with patrols of a different mob type that isn't as annoying. Then it won't look quite so bad to players who dislike Knives.
I used Knives for ambushes and battles in my story arc, but didn't make them a mission of themselves because I didn't need to. If it had been necessary I would have, but they were only one of the players in my plot.
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Melee characters DO have access to jetpacks you know. The nice thing about caltrops, as opposed to other AoE slows, is that you can fly off them. Well, unless you get webbed by a lieutenant, but you can kill those first and....who am I kidding, Knives, Malta and Carnies are TEH HARD and we need MOAR RIKTI!!! 
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Well.. the second problem with knives is if the ceiling is too low you can't fly over the caltrops with hover like in some parts of the crey labs.
Also, I threw knives into one of the underground council maps which means knives spawn in front AND above you, leading to mid-air caltrops which is funny but also really mean.
I find Crey more difficult than Knives honestly, and Crey is the base group in one of the missions. In crey-knives objective battles crey often wins. Arachnos has wiped the floor with knives as well, but arachnos is highly dependent on which boss spawns.
All in all i still firmly believe people get pissed about knives because they're almost absent blueside and only in the late late game redside so you're just not used to caltropland.
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All in all i still firmly believe people get pissed about knives because they're almost absent blueside and only in the late late game redside so you're just not used to caltropland.
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Actualy, I think youv'e got that opposite. I don't remember any arcs with the redside, but encountered them blueside on my first 50 quite a bit. This taught me that I didn't want to fight them with all the other characters I took to 50, so I don't see them all that often period.
Of course, back then a mob of minions would drop so many caltrops that it would crash my poor client (I still had dialup at the time). Personally, I hate any and every enemy that applies slows since I love me some melee characters. Especially when playing a Brute and watching my Fury bar drop because I can't get away from the caltrops this dead group left to get to the next one fast enough.
That's weird. I've never had Knives as an enemy blueside in the late game. I couldn't get away from them redside, though. Every mission seemed to be knives for some reason.
Blueside it was always Carnies or Malta.
To see Knives Blueside do Crimson's and Indigo's arcs.
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My arc is based around the Knives but doesn't have many of them in it. Using this group was kind of nice because it doesn't have its own custom AVs at all and I was able to make one as an ally for the final mission.
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Was just running Carnie/Malta missions yesterday.
Carnies are ok, I've always liked COT, it's the maps that can be a little much.
Frankly, both Knives and Malta fall in the "very annoying" category for me, but only for specific mobs. The former for the caltrop throwers, the latter for the sappers.
For some reason I tend to encounter knives in blueside caves with low ceilings, so both range and melee suffer.
The caltrops slow greaty, but are so very rarely fatal, which renders them just severly annoying.
Sappers play havok with my end, and have potential to be fatal, but so rarely are, so it all just feels like a cheap trick. They make me slow down and check each group for the @#$ sapper so I can formulate an approach. Once I've found the sapper it's no problem....usually. Which makes sappers simply annoying, not overly threatening (unless there are 3+).
Large numbers of either, particularly persistant, are simply not worth the effort for me beyond a single mission. Using a custom group for the base mob and the stock group for patrol or ambushes is fine.
That's my 2 cents
Just putting the question out there:
Certain enemy groups are well maligned. Malta, Carnies, CoT (in specific level ranges) and of course Knives of Artemis.
Certain factions can be dealt with through control (malta, pre-holding the sappers and gunslingers) and certain factions can be dealt with through defensive buffing (knives/cot mez protection) but does anyone feel if these groups are off limits to build an arc around?
Knives, even if you manage to hold the boss (Hand of Artemis) is probably going to toss out the aoe 30 second stun grenade, and all of them are going to throw down caltrops screwing up your pet AI and generally making every fight that much slower.
My main story-driven arc (Guns, Girls and Gills) is not centered around the knives story-wise but it's certainly a large portion and 3 of the 5 mishes have them as the base faction.