TMs as low-chance random held items, maybe? Like, add a low chance for every Pokémon caught to be holding a TM, possibly with the exception of really low levels, or maybe make the stronger TMs only appear on stronger Pokémon.
This would create a new reason to grind, which is basically what any MMO's about in the long run, and it'd make ingame money worth more, seeing as you'd spend a lot more money on Pokéballs. It'd also make sure people wouldn't just end up with 6x Earthquake in their team without LOTS of trading/luck/grinding.