Alright, might as well give my input.
Torkoal: Mid Tier Definitely NOT bottom. I used it in my very first playthrough of Sapphire and after that I was flat out SHOCKED to learn it sucked competitively when I first hit the scene after how well it did for me in game. It's physical defense is actually slightly higher than Skarmory, though you obviously don't get the same resistances. It has the moves it needs to succeed even without resorting to any TMs (indeed he doesn't get any good TMs so that's a good thing). He might struggle on the water routes, but outside of those he does just fine. Everything has been discussed in more detail already so I won't reiterate it, but seriously he's not nearly as bad in-game as he is competitively.
Magnemite: High tier Really, Magnemite's only downfall is that you have to wait until you're halfway through the game to get it, and that it really, really likes eating up Thunderbolt (though it can use Spark if you feel it has to). It'll evolve pretty much as soon as it catches up to your team, it's fast enough for in-game and has bulk enough (and coveted steel typing) to take a few from those who do outspeed it. And it has significantly more power than Manectric after it evolves (120 vs 105). Really the only reason to use Electrike over it is earlier availability. And access to Bite I suppose.
Poochyena: Low tier Mightyena is pretty much only useful for one thing; its dark typing. Before it evolves, it sucks. After it evolves it's decent for a bit, then starts sucking again. But for facing Psychic types, there's nothing better until Absol, who is rare and not until mid-game. It also dominates most ghost types. These factors means that it's good for Tate & Liza (a big deal in Emerald) and Pheobe, which can be troublesome without a dark type. But since both of these come after you can get Absol... Well it's hard to justify using it.
Shroomish: High Tier Comes early and just when you need it, and gets lots of useful status moves (Stun spore, Leech seed, Absorb) and (for the period) decent defensive stats that make it a great stalling Pokemon. This isn't great for efficient runs, but gets the job done. Can beat Roxy like this. It evolves pretty early at level 23, and gains Mach Punch which absolutely creams everything early game due to Breloom's ridiculous base 130 attack. Just when Mach Punch is getting too weak, it gets Sky Uppercut and goes back to dominating. While its Grass typing might be pretty useless offensively due to its low special and low BP moves, it does provide a useful resistance to Water. Probably the best fighting type you can use if you're not starting with Torchic. Doesn't rip *everything* to shreds though, and sometimes even with Mach Punch that speed and late-game fragility will weigh it down. It also takes a lot of experience to level, but does decently even if it's slightly behind in level. Mostly though a great pick.
Gardevoir: High tierWhile it's not the best early game I think people are hammering Ralts and Kirla a little more than they deserve. It hits well enough with Confusion (and later Psychic) to be of some use, if not exactly a massive asset. And once it DOES evolve, well we've all covered how spectacular it is here.
Lotad: Mid tier Totally agree that it's nearly useless early-mid game. Until it gets Surf it sucks balls. It requires a water stone to be of any real use late game too. It does make a damn good HM slave though...
Zubat: Mid tier While it starts out terrible, it does help against Brawly by sheer virtue of it's 4x resistances and Supersonic. Once it does evolve though it'll almost immediately evolve into Crobat and become a total beast for a while. It drops off somewhat later on but it's always a solid member, even if it never stands out too much. Decidedly average overall.
Makuhita: Mid-High tier A Hariyama was my MVP in my Sapphire Scramble, but that was due to the restrictions on my other Pokemon more than anything else. Overall, it has good bulk, good power and good coverage outside of ghosts in just normal and fighting type attacks. It is somewhat outclassed by almost all the other fighting types though, except in availability. Oh, and as a Makuhita it totally sucks, but it does evolve rather quickly at least (level 24). It won't let you down, but it does start to show signs of weakness towards the end of the game.
Linoone: Mid-tier As an actual battler, it's "OK" at best. It's pretty useful early game due to STAB Headbutt, but has no real advantages against gym leaders or the Elite Four and just overall drops off in power. Its real saving grace is Pickup, which keeps it useful the whole game long.
Wingull: High tier High tier just for general utility all throughout the game. It won't sweep the floor with everything, but it does well overall. It can help against Roxy (it won't win vs. Nosepass' Rock Tomb but can inflict some damage at least) , Brawly, Flannery, Norman AND Tate and Liza, which is great for a Pokemon available so early on. It learns both Surf and Fly, giving it utility in battle and out. Take the time to get Ice Beam from the Abandoned Ship and it can help against Drake in the Elite 4 as well, and it has some advantages against a couple of Steven's Pokemon. Considering how early you get it and how it maintains usefulness throughout the whole game while never being a load, you get one hell of a solid Pokemon.
Alakazam: Top I'll be honest, I haven't used this myself, but I would like to say that a mere 4-6 levels of grinding should not take away from the domination it has later, assuming everyone else is right and Alakazam is as good in RSE as it is in every other game it appears in, the 10 minutes of extra training is worth it. If you're argument is coverage based instead... ok we'll see.
That pretty much covers everything I've used except Torchic and Mudkip (both top obviously, very little argument there). I might play some more of this afterwards (it'll be nice to play some Pokemon without having to record everything I do for once).