I've also been a lurker for a long time. Played a bit on shoddy and a bit on wifi, never too brilliantly, but oh, well.
First of all i want to make clear that when i refer to wifi and the wifi metagame, i don't go with "joined randompokechat, asked for a battle, go with it" but with a high level play, as smogon, tournaments on big forums/sites, etc.
I don't really think that the wi-fi metagame develops slower than the shoddy metagame, but, as it has been pointed before, just differently. Not being able of playing with rotom-a means way more than one less poke. Things like SDLuke now can use ice punch / Stone edge as superior options to Crunch because of less chance of a ghost appearing (and gengar failing to resist any of them anyway). As some people have already pointed out, stall is way less useable on wifi, and i don't think it's because of the unpredictability of the metagame, but more of the time factor; playing for one hour is boring even for the stall player. The wi-fi problems adds to this factor, more time for match means more chance of a connection error. I don't think it develops slower as a bunch of players are from smogon, and probably use similar tactics and pokes to shoddy/smogon analysis, but just adapting them to a more fast-paced and rotom-a-less metagame. Heracross is probably better as some of its counters dissapear. Spinners can be more useful as the main spinblocker is also gone.
As a different point, even competitively, people are probably playing more pokemon that they like. If you just wanna play to win/be-the-very-best without caring about what you use (providing it's legal), you have shoddy. More battles in the same amount of time means more chances to win, a way easier and faster method for changing/creating/fixing teams and test them. In Wi-fi, you have to see them for 15-30 mins each combat, and you have probably put some effort on them (unless you sav/ar).
On the other hand we know how shoddy is. Fast battles (even stall wars last for less time than a full offensive battle on wifi), fast teambuilding, fast editing, every option available. Maybe you can even think a bit less and play "test and error", just adding things you consider good and then change them as you test them.
Those points and some more i'm probably missing define a slightly different metagame. If you think different when you are teambuilding, you are obviously getting different results. That directs to a different final metagame. The similarities between them are probably due to smogon's famous tiering system affecting almost every player/forum/site and an obvious quality layer for some pokes.
Going a bit off-topic to the AR/sav discussion, for common battles i just think that saving/editing isn't even logical. If what you want is speed, go for shoddy. You can make your team even faster than with sav. If what you want is nice battles, you don't need the perfect IVs, and EV training with pkrus and the power items doesn't last more than an hour. The only option i see viable is for a tournament, ok, you don't have time to build a full team and train them, but for tournaments, i don't see as an option to allow sav/AR as people who don't own an AR or a flashcard are in direct disadvantage.