Hmm.  Never really thought about them before.  Let’s see…

So, their teams are as follows (movesets and items are generally an improvement on their basic lineups):

Red: As his Heart Gold/Soul Silver team
Blue: As his Heart Gold/Soul Silver team, but swapping Pidgeot for Aerodactyl
Lance: Salamence, Haxorus, Kingdra, Flygon, Hydreigon, Dragonite
Steven: As his Emerald team, but swapping Skarmory and Claydol for Archeops and Excadrill
Wallace: Sharpedo, Swampert, Walrein, Starmie, Ludicolo and Milotic
Cynthia: As her Black 2/White 2 casual team, but swapping Milotic for Roserade
Alder: Reuniclus, Chandelure, Krookodile, Conkeldurr, Braviary and Volcarona

So, Red doesn’t change at all, and Cynthia just reverts to another of the Pokémon she used on Platinum.  It’s odd that Blue would replace Pidgeot, who is his strongest Pokémon on Heart Gold and Soul Silver, but throwing in Aerodactyl instead certainly makes for a more menacing line-up, and fits his obsession with rare Pokémon (although I seriously question his decision to teach it Fire Blast, particularly in a Choice Band set…).  The changes to Steven are, likewise, straightforward; Archeops over Skarmory fits his interest in rare stones and fossils; Excadrill over Claydol gives him another Steel-type to replace Skarmory and helps him to dig up cool new rocks.  I’m really not sure about Head Smash on Archeops with Defeatist to worry about, but I suppose it combos decently with Sitrus Berry and Acrobatics, and I’m glad to see the back of that bat$#!t special attacker Aggron set he used in the third generation games.

Wallace changes out most of his team, keeping only Ludicolo and his signature Pokémon, Milotic.  Wallace doesn’t have much of a unifying theme to begin with other than being a Water trainer; his battle philosophy revolves around grace and elegance, but all that translated to in Emerald, as far as I could tell, was using Pokémon who were a pain to kill, like Amnesiac Whiscash and Double Team Ludicolo.  His new team seems generally more heavy on offence, mostly due to the presence of Sharpedo and Starmie, but I don’t think that makes it any more or less appropriate to him.  I’m not keen on the fact that his Swampert is a special attacker, but I suppose it’s not as bad an idea as a special Aggron.

I actually don’t like Lance’s all-Dragon team much, simply because I was fond of the way his original Gold and Silver team worked around the single-type limitation while still making him very obviously a ‘Dragon Master.’  It made him stick out a bit amongst all the other single-type Gym Leaders and Elite Four members.  Multiple Dragonite is obviously a no-go, but I think I would have gone with a compromise team, replacing Haxorus and Flygon with Aerodactyl and Charizard, and maybe Gyarados over Kingdra too.  Also, Solarbeam on Flygon, particularly without Sunny Day anywhere on his team, strikes me as a… poor decision, especially when he could have just given it Flamethrower or Fire Blast.

Alder certainly gets more difficult by losing his focus on Bug-types, and there was nothing about Escavalier or Accelgor that made them strikingly appropriate for him (I mean, Reuniclus and Chandelure are kind of weird choices for Alder as well since they’re very calm and subdued by nature, but whatever).  Conkeldurr and Braviary appear on his casual Black 2/White 2 team as replacements for Druddigon and Vanilluxe, and I think they’re good ones; they’re more dangerous on the whole, and they fit Alder’s energetic style.  It’s unfortunate that Bouffalant is gone, because he almost works as a secondary signature Pokémon for Alder, sharing his excitable temperament and ridiculous hair.  Krookodile is okay as a replacement, I suppose, and probably stronger.  I’m neither here nor there on Alder’s lineup as a whole.

Well, I can’t really speak for what they will do, mostly since I don’t think they’ll remake the second generation games again.  I can talk about what I think they should do, or what I would do – which is to say “f*ck it” because what Whitney likes are “cute Pokémon” and Normal and Fairy both have those in abundance.  It’s not like she’d be the first major opponent to look outside her speciality; Sabrina has a Venomoth, Candice has a Medicham, Volkner has an Ambipom and an Octillery, the Striaton triplets all have Lillipup, and several Elite Four members are all over the place.  They could even reference the fact that Clefairy was once thought to be a Normal-type until Fairy Pokémon became better-understood.

Also, there’s a fourth possibility you haven’t mentioned – make Whitney a Fairy-type specialist, keep Miltank as a lone Normal-type and give her a different signature Pokémon, like Clefable.  Why not?

I’m not sure whether I’ve discussed it yet or not either.  It sounds like the sort of thing I might talk about.  Could have come up in passing.

I think the obvious answer is that, in keeping with the franchise’s normal stance on what it takes to be a good trainer, most of the grunts for the various evil Teams are just not very nice people.  The more happy and fulfilled your Pokémon are, the more dedicated, energetic and creative they can be.  Most members of Team Aqua, Team Magma and Team Galactic are little more than thugs and may not be giving them the kind of emotional stimulation they need; Team Rocket certainly don’t.  Some members of Team Plasma are genuinely decent people, but most of them are also avowedly distant from their Pokémon because they intend to release them and don’t want to get attached.  Team Flare may have a similar rationale, if they’re aware that Lysandre’s plan for a new world involves the extermination of Pokémon as well as other humans.

Actually, I think the more interesting question is why the Pokémon belonging to the leaders of these groups are not shite.  In many cases it probably has something to do with the genuine charisma of these figures – Giovanni, Maxie, Archie, Cyrus, Ghetsis and Lysandre all have very strong personalities and a great capacity to lead (on top of which, Maxie, Archie and especially Lysandre have legitimately noble personality traits as well – although one must wonder whether Lysandre’s Pokémon know the full extent of what he has in mind).  Their Pokémon may admire them every bit as much as their human followers, to the extent that they can ignore any deficiencies in the affection they receive – and might, through that admiration, come to emulate their trainers’ moral and ethical leanings, in much the same way as Pikachu emulates Ash’s…

Thanks. 🙂  Now, the Elite Four… Hmm.  To some extent I think the fact that they just don’t know what’s going on might play into it; Team Rocket, for example, keep their takeover of Silph Company very quiet until the protagonist bursts in and starts making a mess of everything, while Team Galactic, Team Plasma and even Team Flare to an extent do make some effort to appear legitimate.  That can only get us so far, though; at some point in every game from Gold and Silver onward the s#!t hits the fan in a pretty spectacular fashion.  I think the reason has to be something to do with the differences between the roles of the Elite Four and the Champion, because the Champion normally does get involved in some capacity.  The Elite Four, as far as we can discern, are somehow selected or appointed; they are chosen to represent the Pokémon League and they have very clear-cut responsibilities: they’re supposed to spend most of their time at the League headquarters, ready to accept challenges, and training for challenges when they’re not doing that.  Since they’re always there, they may also have other duties related to the day-to-day running of the Pokémon League – appointing referees and adjudicating rules disputes, co-ordinating public works, overseeing Gym Leaders and Professors, just generally getting stuff done (also, some of them may genuinely not give a rat’s @$$ about whatever’s going on – it’s hard to imagine the self-centred, callous Agatha taking the time to sort out Team Rocket on her own initiative, even if she knew what they were up to – although other cases are less easily explained away; it’s strange, for instance, that Phoebe, whose grandparents are the shrine guardians of Mount Pyre, doesn’t take a personal interest in the Hoenn crisis).  The Champion, by contrast, attains his or her position through a sort of direct meritocracy, by defeating the previous Champion.  Changeovers don’t happen often, but they can happen without warning, and you have no idea ahead of time who the next Champion is going to be.  This is probably not the person you want to be in charge of quotidian affairs.  The Champion is a figurehead; he or she describes vague, long-term “visions” or “missions” for where the Pokémon League should be and what it should look like one year or five years from now, and then the underlings run around and make it so.  The position comes with few actual responsibilities other than “maintain the good standing and reputation of the League,” and the Champion probably doesn’t need to stay at the headquarters because there should be plenty of warning if a challenger looks likely to get past the Elite Four.  As a result, the Champion has a lot more freedom to go on adventures at random and indulge personal whims, including being a Big Damn Hero.  Basically: the Elite Four have s#!t to do.  They’re employees of the Pokémon League with clearly defined responsibilities, which generally do not include dealing with crazy apocalypse scenarios.  Crazy is the Champion’s department.