I think it has more to do with the fact that water areas are a pain to deal with unless you got a ton of repels (which any respectable trainer should) I've always found the water areas to be a chore and slow down process (granted, many goodies and hidden areas are unlocked after getting surf/waterfall etc) IGN did worded that very stupidly however.
As for too much HMs, I agree. There is no reason in this day an edge why HMs have to be battle moves as well. They outta be just items that a pokemon with certain features can perform outside of battle (water pokemon can surf, pokemon with claws can cut, flying pokemon can fly, etc)