Nothing fancy to say up front, here's my list. realized it had two sections, so i split em:
First up, stuff to fix from FO2
1) Fix Inventory - Kind of a mix of everybody's suggestions here regarding carrying weight, backpacks, ammo weighing stuff, etc. Despite what has already been released about hardcoe mode etc, I would love to see carry weight dependent solely on your strength (a bigger bag won't help you carry 500 lbs on your shoulders), and a portable way to carry more (a cart, a vehicle, etc).
2) Repair - seriously took away from the game in FO2 I believe. Shouldn't be able to repair anywhere, should require tools/workbench etc. But on the flipside, why should you have to have an exact (or near exact) match to the item in question to repair it? Scrap metal? Brahmin hide? Come on, let us use some raw meterials. NPC vendors can seemingly repair anything, and I doubt they have a steady supply of Tesla Armor sitting behind the counter at Moira's, and if she does, why hasn't she been letting me buy it? Frustrating to have one of the best armors in the game because I went and got a single suit of Tesla from Mothership Zeta, but since I am nowhere near the end of the main storyline I don't want to use it, because I won't be able to repair it past NPC repair levels for quite some time. On this note, please, PLEASE turn up the item HP. Repairing armor after every single dungeon delve tells me one thing: I have crappy armor. Sure, maybe ghetto rag tag raider armor, but power armor? Combat armor? Metal armor? If power armor has enough fuel to last 100 years, why doesn't the armor itself last that long.
3) Range of items. There just wasn't enough choice among items, weapons more so. It seemed that every class of weapons has one that was "the best" (or in some cases, the only), so there wasn't really a lot of choice, every character I made used the same weapons. And I don't mean make 20 skins of the same weapon, I mean weapons that actually have different feels, uses and stats. Better range, accuracy, damage, effects, magazine size, (mods available? if those happen, which is #4).
4) Weapon Modifications - Some should be pretty simple...putting a scope on your hunting rifle....or a bigger magazine on your assault rifle...gee, I have heard of these somewhere....maybe fallout 2? But why stop there, your game should be better, it has a better engine, new technology, and now you have the best of both, the minds of the old school and the pockets/tech of the new! How about some dirty wasteland mods? Two single barrel shottys duct taped together with a little mechanics thrown in....double barrel shotty? How about some Wonderglue and a prized diamond on the end of a lazer rifle, tri-beam laser rifle? And don't neglect armor mods! Hardened power armor anyone?
5) melee - Make it not svck. really. On that note, fix sneak too. I'll get angry if I go in depth here, so figure it out, you get paid the $$$.
6) Run speed? it may have just been me, but I always felt like I was moving way too slow. I was super excited when I perused the options panel to find that there was a walk/run button, and an option to always run! Only to find out that it had been on the entire time, I WAS running....turned it off for kicks, and apparently found that walking is akin to crawling. Simple fix, it's even in your console commands...which yes i used, and loved. (god bless PC version, despite console sales). On this note, please put a vehicle back in. Not only would it help with inventory realism (see #1), but it would be a better alternative to current fast travel in F03. You could do it either the classic F02 Style and make the vehicle a fast travel point, or actually make the thing move, I don't care. But a champion of the wastes would find a way to travel other than hoofing it around everywhere.
7) better crafting for chems, make it use ingredients, which put out predictable results. Not random (mostly useless) chems once every 24 hours, that was dumb.
8) Power Armor - Had way too much of a feeling of just making it the top tier of normal armor. Power armor was supposed to make a soldier a mobile tank, able to wield heavy ordinance, take insane damage, but have crap for small task maneuverability. If I remember right, the older games took away most of your sneak, repair, and other fine task skill points, while making you NIGH UNSTOPPABLE. The only power armor I truly liked in FO3 was Tesla Armor, and that still needed some tweaking (Tesla was supposed to protect you from energy weapons better....not make you better at shooting with energy weapons...
9) Dialogue. Not sure i have to say this, but it belongs in my list anyways. Not going to explain, because I have good faith in the Obsidian team to do a good job here.
Next up: stuff I would like to see because it's Vegas.
1) Vegas styled weaponry and armor - mob style weapons (tommy gun, billy club, bloody shovel, deringer, etc), and vegas inspired craftable weapons, instead of a bottlecap mine, maybe a casino chip mine now? Turn those old water fountain show pipes into one mean water cannon...watch a super mutant stumble by with a roulette wheel for a chestplate, etc.
2) Old west stuff. it's the desert. Before nevada had neon lights, gambling and women, it had....cowboys, gambling, and women...

I want to see horses, revolvers, lever action rifles, cowboy hats, the whole bit. If you took vegas, and stripped it of infrastructure and technology, it would be the wild west again, only worse.
3) Area 51. You know you wanna...just do it. And please bring back the aliens from FO2, the retro grey's in FO3:MZ were pretty bland and boring, with the exception of the "abduction audio files", which were hilarious sometimes (and other times boring), but mostly hilarious.
That all said (and I'm sure I missed one or two that I will think of later), my feelings for F03 and FNV are mixed. First playing F03 on Xbox 360...I hated it, wanted nothing to do with it. Felt clunky, like i never had enough buttons on my controller, navigating menus was slow, sensitivity way off...these could all be fixed potentially. I needless to say did not buy the expansion packs. Well, this christmas, Steam had the GOTY edition on sale for like 20 bucks, I figured what the hey, everybody said it was better on PC that I knew, and I agree with them now. Also the Broken Steel add on was very much so needed (yay for endgame sandbox play!), and while not groundbreaking, Anchorage and Point Lookout were very well done and I enjoyed them. While I loved the concept and some of the humor on MZ, it was largely unimpressive to play through, and went a little overboard on the retro feel (*@^! rayguns felt like playtoys). I have not played The Pitt, and i'm not sure i will except to maybe get Tribal Power armor which sounds awesome...but I am sure I will be dissapointed with as with most power armor in the game. I have good faith that Obsidian will pull through with a better "feel" for fallout....since it was their baby and all. I will be buying it regardless, because I am a sad, sad little really devoted fan of anything fallout. I am really happy to see NCR in the story, and to see the story back in the desert, not sure why, I just loved the desert backdrop from F02, was the best expression of the theme for me. Good luck Obsidian, and make me (us) proud!