Heh, basically you want a non-thinking game that doesn't only do walking and pulling the trigger for you. Nearly all things presented here are convenience to the point of laziness, and possibly well beyond it. If Bethesda's game isn't Fallout, then your modded game isn't Fallout twice as much.
EDIT: All right, I'll point 'em out.
1) That's why you should have played first Fallouts for. If you didn't, then this kind of reference indicator won't tell you anything because it won't ring any bell.
2) A what? You'd rip the game out of playability for good. OK, now I'll just get 40% Science and 6 Intelligence and go talk to the computer highlighted in my uber-map...
3) Yes, you WANT a quest tracker, in a form of a journal maybe, which says "this guy told me to go southwest. I need to find item X. Hmm. Maybe I can learn something more when I get there." This has some fun in it this way.
4) Nothing against it, though I doubt that people with worse graphic cards will like it...
5) There were never autosaves in Fallout, and that's generally a bad idea. You should remember to save! If you don't, and will be forced to replay some area again, that'll teach you a lesson.
6) Ditto.
7) All right, I admit it. I have no idea what you're talking about here.
8) Yeah. It'd be like: "Go and face the danger of the wastelands yourself, brave daredevil! And don't forget to be level 20 before you go north baby." That spoils it so hard...
9) Breaking gun (like everything else) has always a random element in it, so it should NOT be revealed when it'll happen.
10) Stupid convienience. Most of the time in Fallout no computer even told you "skill too low", you just "didn't succeed" and could try again, hoping you meet the requirement but just didn't pass the check. Like in real life.
11) Agreed to some extent, a HUD with more than HP and AC and AP would be good, though the "xp per hour" thing is just stupid, this isn't hack n' slash (at least FALLOUT isn't.), and the real time clock as well - get one in your room instead. On on your wrist.
12)
(remember this one - it'll come in handy many times later on 
) Yet another stupid convenience. Where's the fun in that?
13) Ditto.
14) Yeah, I always suspected that vault dwellers were so stupid that they couldn't simply read the option and make out if it says "to hell with you" or "hi".
15) Clairvoyant vault dwellers!
16) The ancient rule of "talk to everyone" comes in handy instead. You can figure if they have good or evil quests for you to perform, and then you can decide. That's the fun of RPG games. And you could always change your mind, you know
17) See point 12. You want to find the best way and damage type to kill different creatures yourself - or else go play something else than Fallout. I remember I used to storm floaters with plasma...
18) See point 12 again.
19) A list of people is bad, but as for the locations, I agree. Something like a Fallout-fashioned GPS - but it should be like it points your way on the map and then you have to go there checking the map every once in a while. Otherwise, see point 12.
20) Quite spoiling - you can usually guess what it does, or have it in the description. Without numbers, of course, but as for the exact values, see point 12.
21) You already said that before, if I make out what you're saying correctly. 'Achievements' is a very general term, elaborate.
22) The only point I'd agree with is that there should be a sympathy counter for each faction (though you didn't say that directly). And maybe, for the flavour, the list of stuff you did for/to them. Good ol' Thief: Deadly Shadows...
23) See point 4.
24) In FO1 and 2 you already have the green bar on the right hand side of the weapon image in active slot. I think they won't drop it. As for the general ammo counter - see point 12. The guy just can't think about everything at the same time!
25) As if the pleasure and fun of finding such things wasn't the greatest when you go and find them yourself.
26) Firstly, see point 12. Secondly, how will the game know which items are useless for you? You can preset it, maybe, but then see point 12. Also the vendors might not have enough cash to barter for all of them.
27) See point 12, and generally this is for lazy dumbies.
28) Depends on what you mean - if you mean a map that would show you where entranced to caves are, agreed (but only for the locations you've already been to, except if you buy/get that map from somewhere else). If you mean precise maps for each and every cave - OK as long as you make them yourself by being there, otherwise see point 12.
29) Mostly for shooters fans, but why not, since Fallout 3 will be a shooter to a greater extent than I would've wished.
30) Extraordinarily stupid. The point of RPGs, however perverted can this one be, are dialogues. You can always have a Morrowind-like journal where some good daimonion rewrites all your conversations patiently, mostly for fun when reading it later by the way, but as for "what they will tell you"... see point 15!
31) Why not, although that won't be used much because making your character is such fun. Basically a convenience again.
32) See point 12.
33) Ditto.
34) Ditto ditto!
35) I would very much like to say something poetic or sophisticated, or even creative at the end... but well, I must say "See point 12" once more.
Critical hit on Ghoul " one, with text from or resembling the original text box.
And well, there's a way to convert Maya files into Max. (They taught us Maya instead of Max. Long story.)
, especially the references part, I hate cheap references.