Well, yeah - I guess I agree that that tendency is there, but it's not impossible for a remake to be "true" to the original or even possibly an improvement.
The classics have many skills that were useful but didn't make it in Fallout 3. Outdoorsman, Gambling, Throwing, First Aid, Doctor, Steal and Traps.
The team would have to use scripts to include those skills in. (And how would someone be able to increment them on level up?)
Then you have the SPECIAL system that works differently than Fallout 3. Skills can be boosted up to 200%. This can be easily done indeed, but in the classics, having 100% doesn't mean you always succeed. So there are some mechanical changes that most be done to all skills.
About dialogue, Fallout 3 does not allow long dialogue lines. You are limited to 80 characters for the player's answer and 120 for the NPC's response. It's fine for the NPCs since you can simply add more dialogue "pages" but limiting a player's answer to 80 characters will be difficult to work with. Some Fallout 1 and 2's player's choices could be much more than 80 characters.
You also can't get rid of the [Stat/Skill/Karma/Perk] thing beside some choices.
There must be other things I forget that were in the originals and couldn't be "imported" into Fallout 3.
This being said, though, level design is the easiest to do. As seen http://ca.youtube.com/watch?v=O6WYb0XMmwE to get the hang of the GECK.