Coming off from a near complete "guide dang it" playthrough of FO 2, here's a list of stuff I'd gladly put hours, days and years into improving if I had any clue about modding.
1) Companion system
Playing the game without the "control companions" feature even if it crashes the game is unbelievably reductive. Nothing would frustrate me more than if the next sfall doesn't have the featue even in the buggy state. With companions limited to non-burst weapons and suicidal tendencies - you're better off without most of them frustration wise, and then you need so little gear that rewards lose all meaning.
Flavour of not having companions be just mindless extensions of the main character - fine, but with the AI such as it is... just no.
2) Fallout 2 was really phoned in too much
2.1) The person who said "no radio's" actually had a point. If you could bloody well use a radio to communicate with various people, there'd be no need for mysticism - you could have a quest to bring one back and keep in contact with Arroyo, and you could keep contact with other people and factions.
2.2) Caravan's are another thing - if you could transport groups of people (play it out as a caravan from point a to point b) the overall story of the game would kick ass. You could link various city stories togather and make the whole disjointed and phoned in mess work so much better with just a few quests - which would also provide random encounters and ways to move from city to city instead of just moving a cab.
A few things that it would allow - solving the Broken hills tensions by "moving" the disgruntled humans to redding to replace the miners that the Enclave took away to mariposa. Would give more meaning to both of those towns. Helping vault city install a doctor in the Den to cure the jet addiction (hey, nurse Phyllis wanted to see the world). Settling down liberated slaves - or moving captured ones. Moving a drug operation from new reno into klamath. Helping NCR establish a presence somewhere. Settling Skags from modoc in the temple of trials to grow food while you look for the geck - so much potential for just about anything...
None of this would change the game as is at all and could've been there in the first place...
2.3) Factions! FFS! San Fran is disconected from everything and you meet the Hubologists entirely too late in the game. All the conflicts there feel like an addon and have nothing to do with the game world - except they're mandatory. The Brotherhood of Steel is so entirely wasted in the game it's unbelievable - so is the Enclave. If the struggle was built up by having your clueless tribal do small tasks for strange guys all through the game (in the den and in other places) and connect them to the various "dungeons" to a degree it would make more sense - plus, you'd get a chance to boost your stats earlier if each base let you in after you done it's quest and let you use a keycard. The slavers are a complete non-option, and the rangers lack presence as well. The skags in Modoc are also pretty wasted and didn't have to be...
3) Loot
Way too much loot floating around, and way too many easily accessible shopkeepers selling gamebreaking stuff. Seriously - if you take the quest to take a ride to NCR from Vault City, go there and buy a decent gun, and you just go back, most of the loot for a good while will serve no purpose but to be sold for another awesome gun - even if the drops are a substantial improvement to what you had available before the trip.
And if you stop in broken hills you can do all the quests there, jump over the New Reno, and get upgrades for free for anything.
If you clear out any major "dungeon" and haul everything out - boom goes any semblance of balance.
4) Skills
are all over the place in terms of usefulness. And not just usefulness but ways to increase them - one of the first things a guide to FO2 teaches is that there are skills that you can improve with books so much that you don't need to put skill points in them. I spent a better part of the game with a full 99 skill points bar (with gifted, even), because I didn't need to allocate skill points, and mostly emptied it when something called for a specific skill check.
5) Traits
are also all over the place, as are perks. I remember using a save game editor to replicate the effects of gifted and small frame so I could have fun with other traits on a "do everything character", essentially giving me 4 traits. I didn't want fast shot because I wanted to be able to aim for fun, but then I was left with Good Natured and Finesse as sort of meaningful ones...
6) And the perks
are such that if you had one every level nothing much would change - I'm playing that way right now and all it means is that I have stuff I'd take anyway and some fun stuff I'd never try out AND the stuff which is just interface improvements (Awareness, Quick Pockets). Most are so marginal, and so few are really relevant that if you grab one every level and ignore the stat increases (or gifted) you're not much stronger at all (at the difficult setting)
7) Why in the world is there so little poison/radiation in the game?
Would it really hurt to have at least Gecko be a deathtrap without rad-aways and radX, what with all the goodies and quests over there? Broken Hills are mining uranium, toxic caves are full of goo, etc. It's like it was cut from the game completely, but the weightless and pricey anti-rad-drugs were left around because... what? And all the related perks look like they'd make sense in a game called fallout except they don't...
8) Weapon skills system - coupled with the companion system. Without the use of a "control companions" mod, you have to throw flares yourself - and you probably suck at throwing. Then you have vic and cassidy who are good at small guns, but only one guy, marcus, who is good at both big guns and energy weapons. And no big guns or energy weapons early in a very long game, so there's no real point in boosting them early. Surely there could've been tazers and stun guns which would work as energy weapons with a low-grade battery ammo, and the hunting rifles and sniper rifles could've been non-burst big guns?
9) Weapons/armor system - there's a balancing problem which affects progression. The end-game stuff is endgame stuff. San Francisco again turns the game completely around with stuff in shops that obsoletes anything you could possibly find elsewhere - the gauss rifle does everything better than any other gun (most other weapons really). The only way to buy them? Clear out the "dungeons" which are the only place where you'd really need them. I always somehow manage to go to San Fran because all the other shopkeepers ran out of money (and don't have anything to sell me), but then I leave so well equipped that wherever I go I know I can shoot up the place. This leaves dissatisfaction because there's ussually a lot to do, but the combat is trivial, non-combat is more complicated than simply shooting everybody would be, and I can't try all my toys out. Sure - don't take any of that stuff and you'll be fine, but again, drops lose all meaning, and then killing stuff loses a lot of meaning too, and so forth...
10) Criticals -
honestly, when I was playing it for the first time ages ago I wasn't aware there were aimed shots in the game, because I never made a character without fast shot. But I wouldn't mind if skills other than weapon handling factored into the criticals - first aid, doctor, science, outdoorsman, repair and so on.
Anywho, sorry about the lenght, a full complete playthrough will leave a man needing to unload.
. what I want to say is it would be better to enhance dungeon not to say " oh since fallout's dungeon is bad, its bad game.". I hate pointless dungeons that only good thing is quantity(maybe bad point though 
