Are you not going to transfer all your DS WiFi data to your 3DS?
Anyway, all it'll do when you play on WiFi on the 3DS if you haven't is wipe your Pal Pad and battle records, that's all
For me, sometimes I notice (only with the English version strangely, and only on my DSi), that when the C Gear is trying to make a connection, it lags the game a bit. That could be it
The routes after Route 3 are much more varied. Trust me. Route 3 itself has lots more
When grass shakes, it's a special kind of bit which runs off of a different encounter table and has different Pokemon
Dark grass has higher levelled Pokemon and sometimes results in double battles