1. I agree with the majority of what you've said regarding Magnemite, however these things are not sufficient to push it up to A due to three reasons, type coverage, bulk, and speed. Although Electric is a great attacking type, by the late game it falls off without coverage to support it which Magneton cannot get outside of Hidden Power, meaning Magneton must resort to 2, 3, or 4HKOs with Thunderbolt to succeed. This might be alright, but Magneton also suffers from low speed and relatively poor bulk, which means that it is often taking a hit before it can attack itself and when it does take a hit it will often be a hit that can 2HKO it in spite of the resistance (Walrein's Blizzard for example, even if it didn't have Surf to wash you away). Magneton is a great Pokemon but can't quite reach the top tiers.
2. I firmly disagree with your assessment of Ralts, supported by my own run where it dominated everything (
my run begins at this post). The first two levels are trivial, it takes only a handful of switch grind sessions to acquire Confusion with plenty of Silcoon and Cascoon available, among others. Once it received Confusion it is self-sufficient. Per my run, Ralts is capable of sweeping Roxanne with difficulty from level 13, and sweeps Brawly without trouble at level 16. Once Kirlia you acquire Calm Mind and trivialize the rest of game as Calm Mind patches up the weak special bulk, enabling clean sweeps against Wattson and Flannery. Norman and the level period of 27-29 are the one weak spot Kirlia faces. Once you become Gardevoir the game is over. Gardevoir isn't merely good, it is in my opinion the single best Pokemon for sweeping the game short of Rayquaza (sweeps Winona, beats T+L minus Claydol, sweeps Juan, sweeps Sidney by setting up on Shiftry, gets 4 kills and can sweep some times vs Phoebe, sweeps Glacia, sweeps Drake with 1-2 Potions, sweeps Wallace), with significantly superior sweeping potential to Swampert and superior physical bulk to Alakazam that directly enables sweeps against the likes of Phoebe and Drake. Ralts and Kirlia cannot be categorized as trash by any means, Ralts being able to easily sweep Brawly ensures it an above average placement even if Roxanne is discounted, as does Kirlia with easy sweeps against Wattson and Flannery. With Gardevoir being one of the best three Pokemon in the game once it arrives, it fully and completely justifies its S tier ranking, a belief backed up by the majority who have run it since it was raised to S.
I've looked into your logs with the Ralts and Kirlia period, particularly the first four gym leaders, and, with respect, I'm not sure it's deserving of the praise you harp onto it. To back this up, I'll go through your logs of Roxanne, Wattson, and Flannery and demonstrate what exactly are my problems with them. I understand if this comes off as nitpicking or even a personal attack, but if you're gonna defend Ralts to S based on your logs I feel as if they're open to scrutiny. It's also worth noting that I haven't properly tested Ralts, but I've been playing Emerald for a very long time and have used it many times, so I feel as if I understand what it does well enough to comment on it here. I've also done enough testing in other games to understand what makes a good/efficient matchup and what doesn't, and I'll be using that understanding to analyze your logs. Without further ado:
Ralts: Gets 2HKOed by any of the Rock attacks, but is capable of using their poor accuracy against them. By using one Double Team against each Geodude and having them either miss Rock Tomb/Throw or use Defense Curl you can 2HKO with Confusion and get to Nosepass with +2 evasion. As mentioned in the Poochyena write up, Nosepass loves to spam Harden (and Block) which allows you to comfortably reduce it to -6 Attack and boost yourself to +6 evasion, at which point you can Confusion your way to victory (5HKO in a vacuum, 11HKO with Oran Berry and two Potions). Ran this a couple times and its pretty reliable as long as you can avoid getting hit on the first turn. Might need to use a Potion or Oran Berry of your own to support in some instances. Pretty decent solo effort.
Even if Ralts can very possibly sweep here, this is clearly the exact opposite of an efficient sweep. Having to rely on misses and Double Teams just for a chance to
11hko Nosepass is simply not worth it whatsoever. No one in their right mind would or should go through this much effort for a battle you could easily sweep with your starter, Shroomish, or even Nuzleaf or Lombre.
Kirlia: Voltorb can be used as set up for Kirlia. After a couple Calm Minds the Sparks and Shock Waves do meager damage while Double Team is used to insure against Selfdestruct. Cheri Berry means that when Spark procs paralysis, Synchronize leaves only Voltorb paralyzed. This takes 1-3 Potions depending on rng variance. At +6 Kirlia OHKOs Voltorb and Electrike, 2HKOs Magneton, and is just shy of the OHKO on Manectric while taking insignificant damage from their Shock Waves. With the caveat the Double Team is not deleted, Kirlia reaches level 21 for Calm Mind, and a Cheri Berry is equipped, this is a comfortable clean sweep for Kirlia. Excellent showing.
Again, this is incredibly inefficient. Needing rng to dodge Self-Destrust (which would likely or guaranteed ohko your Ralts), getting up to +6, spamming potions to Synchronize paralyze Voltorb (is that step even necessary?), all to only ohko the two weakest members of Wattsons team? Does a sweep where you need good rng, the max amount of stat buffs, and potion chugging only to achieve a moderate damage output really make for an excellent matchup? Considering you might need around 4-5 Calm Minds to ohko even Voltorb I cannot accept in good faith that this matchup is good, let alone excellent.
Kirlia: Needs 3 CMs to OHKO Camerupt, 4 CMs to OHKO Torkoal, Numel will use Sunny Day and can then 3HKO with Take Down or Overheat. Needs 1-2 Potions and then clean sweeps.
Not a lot to say here since the log isn't very descriptive (not necessarily a bad thing, just sucks for me) but I'm curious as to how exactly you were able to ohko Torkoal with just Kirlia. I did some novice calcing and it doesn't seem to quite click for me:
+6 Lvl 21 0+ SpA Kirlia Psychic vs. Lvl 29 0 HP / 0 SpD Torkoal: 71-84 (80.6 - 95.4%) -- guaranteed 2HKO
This calc assumes a + sp att nature and max ivs in every stat. I didn't see your Ralts ivs if you posted them so I can't be sure of what they were. I'm not accusing you of lying or anything, just curious as there may be some factor I'm missing here. I'm willing to accept this as a good matchup for Gardevoir, as this is well within the level 30 range to have Garde, and then the calcs become much more in your favor:
+2 Lvl 30 0 SpA Gardevoir Psychic vs. Lvl 29 0 HP / 0 SpD Torkoal: 107-127 (121.5 - 144.3%) -- guaranteed OHKO
Far less setup necessary for a much better result. Based on this I would not rate the Flannery mu based on Kirlia; the few levels of grinding definitely pay off for the far better sweep.
Overall I don't find your defense of Ralts to S, based on your logs, to be very convincing. You rate it this high based on an egregious amount of stat buffs that are just inefficient and not very reliable to obtain. The Ralts and Kirlia period, based on your logs, is very contingent on luck to obtain ok results at best. I should state that I don't really have an opinion on whether Ralts should be S or not; I recognize both sides of the argument and think they both have a lot of merit. But I simply don't see the evidence that the Ralts and Kirlia period is as good as you claim it to be.
EDIT: I forgot to change the level for Kirlia when running those calcs vs Torkoal. I called them novice calcs for a reason

that part can be ignored. Otherwise what I said about Kirlia vs Gardevoir there stands.