I've been replaying Heart Gold recently and the following things about it are really grinding my gears:
* There are too many boring Pokemon. Every route is just a plethora of com-mons with maybe one cool unique guy who's only got a 5% chance of appearing.
* The fact that the game get harder as your team gets bigger. Instead of one team member hogging all the exp and getting overpowered, now you're trying to distribute it among six guys and falling short.
* Everything between Ecruteak and Blackthorn is too easy. Then there's a big difficulty spike when you get to Clair's gym. This mainly ties into my previous problem, where everyone on my team is underlevelled because they haven't had a challenging fight since Sudowoodo.
* Voltorb Flip doesn't work! Apparently this is a problem with copies of the game sold on eBay for some reason, so it's more my problem than anything else. It does mean I can't get any of the best prizes.
I think I've just been a bit spoiled by the newer games. There's still fun to be had with it, but I'm starting to miss the reusable TMs, the wide variety of awesome Pokemon and the Exp Share that affects your whole party.
I actually played through Diamond all the way through the E4 for the second time since I've completed the Dex. (Meaning I had to get rid of 400+ hours of play time and trapping 'Mons in the ranch forever ._.) It made me think that it and Pearl get way too much flak then they really deserve. Yeah they're painfully slow compared to the more recent ones but I quickly got used to it. Yeah I still prefer the Gen V games by a margin but it was better than people give it credit for. Also planning to replay HG eventually with a Rotom and a Finneon.