Okay let me start off with stating I'm not advocating turning TTW into Fallout 3 2.0 however I do like the fact the next version of TTW will have fallout 3 style repair as optional, the rock-it launcher back and will have the big guns skill returned as either part of the base game or optional. Those are 3 really great things in my mind because they add to the game. With that said New Vegas did somethings better like different ammo types, basic weapon modding, deathclaws being really dangerous, companion wheel, etc.
However while New Vegas did improve things by copying what the fallout 3 modding community enjoyed (they openly admitted to doing that and were smart to copy popular mods) somethings Fallout 3 still did better imo. The first being Energy Weapons being more powerful in Fallout 3. The plasma rifle only consumed one microfusion charge in fallout 3 and was much more powerful in that game with the way mechanics worked in Fallout 3 compared to how mechanics work in New Vegas which makes the plasma rifle much weaker. The plasma rifle was not the most nerfed weapon however that would be the gauss rifle which requires a whopping 5 microfusion cells per shot making the thing detrimental to use often since it just eats up way to much ammo compared to the fallout 3 version.
Feral Ghoul Reavers in New Vegas are also pathetic compared to Fallout 3. In fallout 3 if you run into a bunch of feral ghoul reavers that could equal you being killed. Feral Ghoul Reavers were tougher then Deathclaws in Fallout 3. Since Deathclaws were made dangerous in New Vegas it would be nice if Feral Ghoul Reavers went back to being dangerous as well like they were in Fallout 3.
The Karma system in Fallout New Vegas is beyond broken. You can make arguments about how karma worked in Fallout 3 but in New Vegas it was done half assed at best (you can murder everyone in the game and end up with very good karma) and that the developers really didn't care at the end of the day. In New Vegas it's all about factions which work for New Vegas where is in Fallout 3 is really about morality. In TTW you are the lone wanderer and you become the courier after going to New Vegas. You weren't raised feral you were raised with morality particularly Judeo-Christian values with your father quoting the bible and a bible reference being a major factor in the main questline of fallout 3.
Since TTW uses New Vegas karma in the capital wasteland and environments in TTW the karma system is also broken. For example in vanilla fallout 3 if you side with Ashur in the Pitt and put down the slave rebellion you get massive negative karma from that since what you are doing is evil. You can do the whole ends justify the means with Ashur using the steel mill to rebuild but that doesn't change the fact that what you did was wrong. However in TTW you take no negative karma hit for putting down the slave rebellion. The point I'm getting at with this is that in Fallout 3 the game choices were morality ones and it would be nice to have that come back. Also it would be nice to fix the disaster that is karma on the New Vegas side as well I mean really killing some fiends trying to murder you isn't an act of selflessness and kindness no it's just fighting back in self defense.
Now I know the idea of unnerfing energy weapons in TTW has been kicked around and I know that enemies are being rebalanced in 3.0 so maybe Ghoul Reavers will be deadly again. So maybe the first two things will come back in TTW. Yet the karma system is the one I really never see discussed and of all my gripes with New Vegas this is my biggest one. I'd rather they would've just removed the karma system in New Vegas instead of ruining it like they did.