You underestimate my pessimism. :P
HG/SS:
1. Gen 4 takes ages to reduce HP after an attack. I didn't actually notice this until it was pointed out to me, now I can't help but notice whenever I revisit these games.
2. There's too much content locked behind events. Really would've loved to have experience the Celebi or Arceus events for myself rather than jealously watching them on youtube lol.
3. The Johto Gym leaders should've had tougher and more unique parties. For example give Falkner a Noctowl, Bugsy a Ledian and Ariados, Jasmine a Scizor and Skarmory on top of the Pokemon they already had. They certainly beefed up the Gym Leader's parties when rematching them post-game but their initial battles were still too easy, that was one of my complaints with the originals too. I'm aware that some of the Elite Four had the Pokemon I suggested but they could've changed their teams around a bit too.
5. Competitive breeding, while still easier than in gen 3 and 2 thanks to certain items, is still way too tedious and time consuming. If you plan on taking on the Battle Frontier you need to dabble in this at least a bit so I wish they didn't wait until gen 6 to streamline the process.
6. Needing Rock Climb to reach the top of Mt. Silver and battle Red. Nobody likes using HM slaves and needing one just to reach the endgame is such a waste of a slot. You don't even need to use flash in G/S/C if you used a guide like this (
https://hieroxiv.livejournal.com/7831.html) which shows you how many steps you need to take and in what direction. It's not as difficult as it might look on paper.
Some additional minor nitpicks:
You can't rematch the trainers on the S.S. Anne which makes the option to board it again pointless when you can just fly around the map. The S.S. Anne was my favorite way to level up my weaker Pokemon post-game in the originals while earning a bit of money.
The Pokemon follow feature, while very cool, should have an option to be turned on and off whenever the player wants. Some of the sprites haven't aged well so I don't always feel like looking at my lead Pokemon.
I think they could've created a better version of Cinnibar Island. Yeah it was destroyed but they had the technology to show the wreckage and debris this time around which wasn't an option for the originals due to hardware limitations. Also if there's a functioning Pokemon Center there then there's no in-game reason why they couldn't rebuild some of the other buildings. Maybe just have the Mansion and Gym destroyed.
Lyra is a poor woman's Kris. This is entirely personal preference but I'm sure most of us can agree that Kris's blue hair helped her standout. Lyra has the most bland design of all female MC's, possibly all Pokemon MC's period.