Above post reviewed at tl;dr's request.
With wifi you have to make your team and not look back. What do you do if you find out your team is weak to a certain mon or playstyle? Welp too bad, time to go do repetitive breeding until you get a new mon to fix the problem.
The primary purpose of Wifi battling, I feel, is not to win. That would be a completely unrealistic goal, due to the reason stated in the quotebox. Oh, sure, you aren't going to just go willy-nilly into the fight with just 6 random members; you will build your team to win. But if you find out your team is weak to something...no big deal.
But that isn't to say you shouldn't keep your options open. I have almost 90 EV trained Pokemon in my boxes, and at least half of them are level 100 by now (and therefore ready for battle). I mix-and-match very frequently.
Let me speak from personal experience when I say the actual battiling on the handhelds is frustrating. I've only built two teams on my DS (one of which is stall and the other is hyper offense) and played about ten games. The first team I played was stall, one of my favorite playstyles, and let me just say that it was /horrible/. Not only was it hard to find an actual GOOD player to face, the battle was also /so/ boring. Half of time I had to stare at the HP bar take ten seconds to get to fifty percent and back up when I used Recover, half of the time my opponent or myself would disconnect 75% into the match. After that I picked up hyper offense, but I strongly dislike that playstyle for a few reasons. Even though my matches were quicker, they still took a long time. Don't get the idea I'm just complaining here from my own experience. A lot of people actually have had the same problems.
I'm not going to deny this whatsoever - by contrast, I am actually going to affirm this. The animations and such I see over Wifi is something I wish that can be turned off, because they're so utterly unnecessary. Were they turned off, the match time would probably be halved. Connection is another tricky problem you have; you need to make sure that both of you have a good connection. (Oh, and Team Preview. We need to get rid of that garbage for full-on 6v6 fights.)
And, of course, there is the matter of finding a match to begin with in the first place.
I am very aware that there are few people who battle on Wifi regularly. As a result, I rarely get any time to brush up my team, if at all - and the opportunities I do get I exploit. I've only ever had 2 Wifi matches - yeah, you heard me right,
2 - and I've learned quite a lot from both of them, on what I should do in regards to my team and playstyle. One of them was, bar none, the best game I've ever played...even though I lost 2-0 (and it should have been 4-0, but Flinchrachi is not to be underestimated).
Now let's look at simulators. For starters, it's so easy to find a battle. If you go on a large server like Smogon and click the "Find Battle" button, you'll find a match in maybe five or ten seconds. I'm probably stretching this statement a little, but you can do almost a year's worth of wifi battles in one month on a simulator. Not only that, but it also lets you test teams more easier. If I find a problem with my team, I can easily go into team builder and fix it.
I'm pretty sure the reason for that is the ease in actually putting a team together and the advertising that goes into it - it's actually directed straight to the fanbase. I don't think this is Wifi's fault at all. If more people were actually interested in Wifi, this problem would either be lessened or just not exist.
Cheating is also nonexistent due to clauses.
You can remedy this completely if you know who you're fighting. Besides, there is always the "Off" switch.
Simulator battling is also a great way to get social with people. On a wifi match, you can't communicate with people over the match, but on a simulator you can.
Things called "voice chat" and "premier events" do exist, you know. Don't think that there's zero socializing involved in DS games. I'm sure you are aware of the existence of Pokemon TCG leagues? People bring their DSs too every now and again.
Don't get me wrong here, I hear that showing people you managed to get a shiny, flawless Pokemon will instantly show a great deal of hard work. I guess that all wifi has going for it - showing off. Not saying that's a bad thing btw.
I'm pretty sure this is probably the main selling point of Wifi battling and such. Teambuilding on DS and teambuilding on a simulator require the exact same amount of thought. However, with DS there is actually work involved. Showing your good win record with a simulator team is no big deal. You can just be "netdecked". Those results can't really be replicated very well with a DS team. Each Pokemon is unique in this way. And the one who has not only the best strategy, but also the most time to burn...effectively has the last word.
(Also I'm vehemently against the RNG method. If you want flawless stats so badly, go fight on a simulator and leave the rest of us alone.)
In closing: I've said a few times that my refusal to use a simulator is primarily due to personal/aesthetic reasons, and not a slight against any particular group of battlers. I just feel that my team is much more "alive" to me than it would on a simulator. Flawless stats and team matchups is not the point - having fun is.