HG/SS ARE the best versions. That said, extra improvements could have been made along with what has already been achieved, to enhance the generational upgrade to Gen 4 further. For me, these include;
-No Sneasel or Houndour before Elite 4 (as was missed in G/S/C)
-Gym Leaders original teams not updated to Johto-Specific pokemon, save for Miltank, Steelix, Piloswine and Kingdra. Why not showcase a level 13 Togetic and level 9 Hoot-Hoot for example?
-Safari Zone. Its non-appearance in G/S/C was annoying, but now its just farcical. Its re-vamped and in a new location, which is cool, but then Pal Park is inserted in Fuschia. WTF? Why not vice-versa?
The seemingly easier encounter rate of Entei/Raikou. I played through Gold for 180+ hours before I encountered Raikou, and I didnt encounter Entei until after I beat Clair. It added to the majesty of obtaining these guys; now you can just look them up in your PokeGear.
Specific factors of HG/SS that annoy me start from the the Pokewalker. In theory its an awesome application, but it has too great an effect on early teams. For example, my current SS team consists of Murkrow, Kangaskhan, Elekid, Magby and Dratini, alongside Croconaw. It takes the magic out of the game progression. Although, our teams can be more diversified with greater options, I suppose. Other PW annoyances are;
-Number of steps needed for non-workers. I work 10 hours a day and take 16000+. 9 year old Jimmy quite possibly couldnt achieve this.
-Your PW Pokemon doesnt gain any level-up moves, and
-You have to return your PW Pokemon each day to receive the level-up.
Also, the improvements that should have been made from Platinum. There should have been an increase in boxes, so that you can catch and store each Pokemon, and formes and Unown, and still have space to store Pokemon in-training or Shinies. But my biggest annoyance is this:
If Gamefreak were planning on releasing HG/SS, then firstly, why did we have to capture all of the Johto Pokemon in DPPt? Now, having achieved a full dex without obviously Celebi and Deoxys, I have to do it all over again. And now there are Sinnoh Pokemon to catch. *grumble*
That is my rant. I hope the fact that I love HG/SS is not missed, however. But, I do have a question: If I have max-EV trained a Jolly Weavile with, lets say, 24 Speed IVs, then bred it for an egg, does the egg IV increase, or stay random? And how would this transend into breeding in HG/SS?