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It depends on whether you play Maelstrom or Eternal war imho.
For Maelstrom I'd say skitarii are better suited.
Skitarii have some very mobile units, namely the Sicarians, adding 3" to move, run (which they can re-roll) and charge distances. On paper, they're rather durable with a 4+/6++, 2W and 5+FNP altough from my experience, you shouldn't rely on the 2W and FNP too much because their T3 is doubled quite easily by most armies. Infiltrators can mitigate that a bit because they have stealth.
If you can get bigger threats on the board (which is hard, believe me people want those units gone), and they have to use their small-arms fire to deal with your Sicarians, they'll probably cause a lot of trouble. Infiltrators will kill most units (or at least severely dmg them) in one turn. However, it's still a good idea to evade dedicated CC units that have Str 6 or higher, especially if they're durable (like thunderwolf cavalry). The Sicarian killclade (1 unit of infiltrators and 3 units of ruststalkers) might be a very good (but pricey) formation for the purpose of objective grabbing.
On the other hand we've got the Cult mechanicus, which I think'll be better for eternal war. They've got a nasty formation consisting of 2 units of katahprons and a dominus. They're kept in reserves and have to deesptrike. I think you roll 1 die for both (although I'm not 100% sure, don't got the book atm). The dominus deepstrikes first and if he deepstrikes within 6" of an objective, he doesn't scatter. Then if the kataphron breachers deepstrike within 6" of the dominus, they don't scatter either.
Now I haven't exactly run the math on this but I'm pretty certain (at least) 6 Str8 AP1 shots (which cause D3 wounds/HP) + a Str8 AP1 blast is going to remove a wide array of units even though most of the shots'll be BS3, because canticles. On top of that they're a very durable unit, sporting T5, 2W and a 3+ armour save. They can easily hold an objective for a few turns (maybe even 2 if they're 12" apart because they're still 3 units).
Now I'm not saying that skitarii can't perform well in eternal war or that Cult mechanicus can't play maelstrom well. This is just my view on the matter and I certainly have experienced one is better than the other depending on the type of mission.
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