Well, I don't see why it'd be that different to the local battles, then. Local battles have the full range of battle options (single, double, triple and rotational) and defaults to full teams and level 50 all (which does increase your level as well as decrease it).
I haven't been able to use the WiFi version yet, 'cos I'll have to wait until I get the 3DS, but I really can't imagine they'd have finally fixed the local battling only to pass on the old problems of it to the online set up.
The manual seems to indicate that the options are the same for WFC as they are for local (single, double, triple and rotational), plus an extra option on whether or not to use the Wonder Launcher (which you don't seem to get a choice over for local). I guess you can't select whether to be level 50 or level 100, but I very much doubt they don't up-level you to 50 for online as they do it for both local and battle subway battles.