The G/S/C Safari Zone needs to be included. It's been said countless times, but it was intended to being the games, but there wasn't enough time/space/whatever to implement it.
Evolution woes? Well, I've heard rumors (I can't be sure they're true, but I'm 99.9% sure they are) that there's a hidden button on the DS called the "B" button, and when you press it while your Pokemon's evolving (unless you're using a stone), it won't evolve. Pretty useful, huh?
Graphical woes? I'd have to agree with you on this one. I don't like the D/P/P style as much as the R/S/FR/LG/E graphics, but still, this is a modern upgrade, so it has to be expected.
Without the Pokegear, the game would be like chocolate milk... without the chocolate.
You don't want your Pokemon to learn certain moves? Here's a thought- don't let them learn said moves. And if you happen to catch a Pokemon with a "non-nostalgic" move, then just get rid of the move, replace the move, etc.
The names? While I can agree that HeartGold isn't exactly the best name, the only time you're gonna see the name is on the box and the title screen. Is it really something to complain about?
I'd like most (if not all) of the features that were added in Crystal to be included in the games. Buena's Password was awesome, the additional Suicune sidequest was great, and all of the Eusine stuff was pretty fun. And if you don't like the Crystal features, then just ignore them. It's not like you're FORCED to catch Suicune.