I'm atleast thankful my brother chose Totodile on his HeartGold version, because it would've otherwise been impossible to get Chikorita any other way since I could not mark it as seen on my file. Also at first I thought the underleveled trainers was a good thing but by the time I hit the 8th gym it hit me on how stupid that idea was because it forced my team to be seriously underleveled and because every training spot I had at the time was underleveled it almost felt as if I were forced to trade in my Rayquaza from Platinum, and even then because I was constantly underleveled I ended up wasting all my money on potions, full heals, etc and I was forced to use my Master Ball on Lugia instead of trying to enjoy the challenge of catching it. Everything after the first battle with the Elite Four was disappointing, because since you had enough badges to have every Pokemon obey you, there was no real point in doing Kanto because you could easily do it with a level 100 traded in from another game. Honestly I wish I could atleast erase my file and start all over to see if I can manage to do it without cheats, but I have far too many important Pokemon on my file already and it would take too long to trade everything back to Platinum, though once I get White I'll send everything over to that file and erase my SoulSilver file to reattempt everything.
Edit: Oh yeah I forgot about this. The 4th Gen introduced Pokemon that evolve from past Pokemon and or evolve at very specific locations such as Mt. Coronet. Game Freak neglected to add substitute locations for those Pokemon in HG/SS and thus certain Pokemon such as Glacion, Leafeon, Magnezone, and Probopass are unobtainable in HG/SS unless their previous forms are traded over to any Sinnoh based game, which I find partially annoying but not really important in my eyes because a complaint like that would only be a complaint to those who didn't have a Sinnoh based game.