Miss Fortune is one of those champions that doesn't seem to have a great set of rune choices. I'll try to outline the difficulties.
Precision is the usual primary tree for most marksmen, but Miss Fortune is less of a traditional crit carry than her peers. Precision has a ton of attack speed built into it and barely any %damage or flat AD (the only example of the latter being Press The Attack, which conflicts with her tendency to switch targets for Love Tap). This path provides her with relatively little benefit and is especially bad for Lethality MF.
Sorcery is one of the other choices for a primary damage path. Sorcery has some pretty cool options in the smaller runes, but all of the keystones perform terribly on her both in lane and out of it. Summon Aerie is weak and she can't use the shield aspect at all. Arcane Comet is incredibly unreliable with her more interactive Q-max laning phase, and her E-max laning phase is weak, boring, uninteractive, and still can't even make Comet land reliably. Phase Rush is probably the best option here, but her playstyle usually relies more on burst or good teamfight setup instead of brute-forcing people down in an extended chase. It mostly helps her kite better.
That leaves Domination, which probably has the best keystones options for her right now. Dark Harvest is a strong snowballing/scaling option and Electrocute gives more reliable early power. Predator is probably the worst of the three on her but still gives her a decent assassination option. However, the last two rune slots are lacklustre. Cheap Shot and Taste of Blood are decent options, but Cheap Shot can't really be used in lane without using E (same problems as Comet) or in a gank/all-in, where it offers little damage. Taste Of Blood is probably her best bet, but not as an aggressive option. However, Sudden Impact's Lethality being locked behind a dash/blink/stealth kind of feels insulting. Her fellow dashless Lethality marksmen (Varus, Jhin) both make better use of Precision as a primary path while Lucian can access Sudden Impact without burning Flash. The Bounty Hunter rune slot also offers her very little: all of her spellvamp-able spells are AoE (may be a bug since her Q is apparently supposed to proc spellvamp according the wiki, but doesn't heal her at all with this rune last I checked), she typically doesn't buy many impactful item actives (Youmuu's is probably the best use of Ingenious Hunter), and additional out-of-combat movespeed is weak because Strut already provides her with so much.
Resolve (rightfully) offers very little, and Inspiration is cool but relatively ineffective because her average autoattack range makes her a mediocre user of Hextech Freezeray, meaning it doesn't make up for the lack of damage in the rest of the path. Secondary trees tend to be fine because Sorcery, Precision, and even Inspiration all provide MF with some strong options without locking her into a subpar keystone. Anyway, that's enough about MF.
General rune impressions:
Fleet Footwork seems extremely weak. The change from %total AD with crit scaling (Warlord's) to low base values with terrible scaling in general is a perplexing choice in direction. Maybe I'm not seeing who this would be useful on, but with Press The Attack for AD toplaners and Lethal Tempo for marksmen, I don't know who else would even consider this. I'm tempted to say that Taste of Blood is almost as powerful as this keystone with its better early values, better scaling, and only slightly longer early cooldown.
Presence of Mind obscures too much of its numbers even in the detailed tooltip. Mana return values would be appreciated.
Dark Harvest seems pretty strong, but I'd like to see some clarification of the fact that deaths of relevant units on both teams (e.g. allied champions and cannon minions) also grant souls. Not sure if this is intended, so I'm asking for either a bugfix or tooltip change to specify this behaviour since typically only enemy deaths grant rewards. If it's not intended, the numbers on soul scaling seem to be quite low.
Arcane Comet seems really unreliable if you don't have hard CC. Not sure how this can be fixed; maybe make it slightly faster so that slows are more reliable in making it hit? Also, it's a pretty boring keystone. Not much interaction for the user other than "land your cc ability" or "land any ability and hope for the best".
Celerity's damage scaling seems weak. Even in extreme cases, 8% of bonus movement speed seems to have very little payoff in terms of offensive stats. Perhaps most of the power was intended to be in the 3% movespeed bonus? The fact that I wouldn't even consider this on MF seems a bit strange as a champion with 100 bonus movespeed in her kit.
Absolute Focus's tooltip is misleading. Last I checked, it did not scale linearly but instead gave something like a 5 AD buff at level 1, 7 AD at 6 and 11 and 16, and 2 AD at 18. I think smoothing out the curve is the simplest solution, but otherwise I'd like to see the tooltip reflect this. Not sure if Waterwalking follows the same pattern; didn't test that one.
Scorch also seems weak, particularly in late game. I recognize that this rune is probably not meant to be a late game rune, but its early impact is also somewhat negligible at the moment. I'd like to see its niche sharpened to focus on early game or to give it better scaling to compete with Waterwalking or Gathering Storm.
Waterwalking is a cool concept but I wouldn't use it in practice. It feels like a rune I'd want to try and play around, but the bonus AD/AP values scale so slowly that it feels like a waste of time to do so. The movespeed for roaming feels most relevant, but 25 roaming movespeed in the same slot as Scorch and Gathering Storm feels lacklustre. I'd like to have it scale to its maximum value sometime in the midgame so that you get the most value out of it during dragon/herald fights, when you spend the most time in the river and to differentiate it from the late, late game scaling of Gathering Storm (and if it already scales like that, I'd like to see that in the tooltip).
In Resolve, Iron Shell and Mirror Shell are so weak that it doesn't feel like I'm making a major tradeoff for always taking Conditioning instead. I'd like to see the secondary effect on Iron Shell and Mirror Shell provide extra flat resistances instead of 5%.
Lastly, I didn't really like Kleptomancy as a concept. I don't think gold income is a "cool" effect, and the RNG aspect of item looting is highly undesirable.
Other than that, I'm really liking the progress on runes. There's still a lot of improvements that can be made, but the overall direction is really cool and much better than old masteries. There are some sacrifices on certain niche builds on old runes, but I think that the gains are overall more than worth it.
EDIT: I've been reading some of the other replies in this thread and and someone mentioned that there isn't a great keystone for DPS-focused spellcasters (Karthus, Kayn, Rumble, Malzahar, Fiddlesticks, and Singed being some examples of champions I've seen fitting this pattern). Seems pretty accurate to me since I've run into the same problem with MF though she's actually better off than most of those champions; there's nothing really similar to DFT in the new runes, which seems to have left a gap behind.
Something that fills the lack DFT does.
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), and the tank update that league overall is worse and it would have been a better use of time to correct the fallout of those things instead.
