I can answer most of those
You have to remember that the alpha was only reached on Jul 15 so this info is pertinent only to the current state of the game which is still far from final.
1 - they work pretty much the same as Generals - the 'super weapons' are now spells which are generated OCLs. They only include the Eagles, the Balrog and the Army Of The Dead ATM.
2 - Not yet - theres no need in the game. Time and resources wont be spent on doing something thats not even planned for or required - see final note though.
3 - No, theres no vehicles, so again its not needed.
4 - Yes, locomotors have been redone a lot to support the revamped AI interface - for example, the Nazgul have to dynamically adjust their flight path gradually as they fly towards an obstacle in order to reach sufficient altitude to fly over or around it. They then reduce altitude appropriately after negotiating said obstacle - when adjusting this angle they flap thier wings more or less so they look more like 'real' thing and this underlines the key difference between Generals and BFME - theres no machines or technology so things have to look like they are 'living' and thinking. So the short answer is that angle of ascent and descent is a variable.
5 - No way, the only missiles are arrows and bezier paths are used for large projectiles such as ballistas and siege weaponry. Other than that the only other missile is a rock that Ents can pick up and throw.
6 - Not known but many things are planed in the pipeline.
7 - Yes, Harvard confirmed this - it was shelved from ZH but remains a part of BFME as one of the ways in which to improve the online experience.
8 - No, there are in fact less specific ways to die in this game than there were in Generals.
9 - Sort of, but this is more linked to the 'animosity' system which generates the unit emotion. In your terms, it will look like 'if attacked by a specific KindOf then ConditionState = FEAR'
10 - Nope.
11 - Same as! Additions to the core engine are necessary to support the new game features but again see note below.
12 - The game will inherently support the -mod command line switch. There are no further plans at this time. The focus on a LOTR game is on allowing community members to participate and recreate in the world of Middle Earth which IMO looks like allowing greater support for maps as opposed to full blown mods. But you will be able to import the games enhanced AI into your individual maps.
13 - It depends if anything is removed from the engine. If the planned vehicle moves with similar rules to a siege tower (which is a 'vehicle') then yes, this is possible.
14 - Same proprietary file formats.
15 - Thats one for the community to decide

Its as extensible and editable os Generals or ZH.
16 - Updated WB will ship with game. Theres no beta, no pre-release of editor.
17 - Most models are around twice the scale and poly count as Generals with the default camera angle zoomed out more to maintain the impression of scale and allow the player to see more of the action.
18 - Same texture format, aspect ratios have to be maintained for optimal rendering by SAGE but they vary with 1024x1024 being the largest IIRC.
19 - In simple terms, I can answer this by saying that if right now you ported a ZH mod into BFME then it would like a Tiberian Sun mod that was ported into Red Alert 2 and would need the same degree of INI tweaking to make it happen - there would be a noticable difference in the scale and appearance of the objects - compare the voxel quality of TS to RA2 and you see what I mean. Thats a pretty good analogy of what a conversion will be like.
20 - Oil Derrick/Black Market code is the same, its used in game right now.
21 - Yes, but radically changed, its used on horses to avoid a horse spinning 90 or 180 degrees on the spot to change direction.
22 - Yes, but upgrade removal usually occurs only as an event triggered by the destruction or removal of an object. There are no player upgrades, only object-specific ones.
23 - No. Buildings levelling up is a new module that triggers the use of veterancy specific condition states.
24 - See final note.
25 - The code at this time is unchanged, however its implementation is very different. A civvy building in BFME may take the form of a larger cluster of objects such as a small forest where you can hide ('garrison') archers for exmaple.
26 - Yes and no. See final note.
27 - No, although the events that it triggers can be modified and edited (it is essentially a GUI to Campaign.INI). The map is a complicated high definition model so if somebody proficient enough wanted to they could create a new one to replace the one in the game. You can edit the 'hotspots' through an INI file, i.e. whereabouts you click to trigger the start of a mission etc.
28 - Both.
29 - There are some air units but the vast majorty of the game is land based combat. Some cinamtic sequences allow for some units to traverse water but this will not ordinarily be possible in game.
30 - INI and map. Map contains the generic AI, INI controls who.
31 - Yes, high veterancy units are merged into your persistant army so they can fight another day.
32 - Yes, special NPCs are represented as Heros in certain missions where there presence and actions have a direct impact on the storyline and its outcome.
33 - No.
34 - Theres a good video on this on the official site, but what you wont see is any unit penalties when an object is in fear of something. This is a gameplay decision because otherwise you end up in the situation where units would possibly refuse to fight or be at such a disadvantage that it wouldnt be worth fighting with them and this detracts from the player being in control of the action.
35 - 3 - the Balrog has 3 attacks.
36 - No. The way it works is that certain objects can interact with others such as stone structures or trees in order to use them as weapons. Ents and Trolls are two exmaples.
You can have new armies appear on the world map model after specific times - this is a 'safeguard' that Mark Skaggs insisted on to avoid a disaster situation where players would have to few units or too small an army to continue the storyline.
34. Same as, but as youd expect there will be some changes.
35. No.
36. Its the same.
37. The guys will watch the community closely and already are - a lot rests on the success of a LOTR game!
38. See final note.
39. Users will get the same tool the dev team use.
40. No, but there will be community support.
Can We Expect Animated Cameo's What formats? *.AVI *.MOV or *.W3D *.BIK
- Nope - there are no cameos right now, the Command Bar has gone!
-Tank Treads and Wheels Like BattleField 1942 ''when its moving the treads and wheels are rotating''
- No, why would this be implemented in the LOTR universe?!
-Multyple Turrets for tanks more then 2
- Ditto.
-3DS MAX r4,r5,r6 Supported Export And Import Tools
- Nope.
FINAL NOTE
The game has only just reached alpha so nothing is final. A lot of the questions are fantastic ones but you have to remember that the team is developing a very specific product based on a very specific and pre-defined storyline. As a result, the way the game is coded will reflect that. In simple terms, it would be rather like making the transition from TS to RA2 - same engine, just used slightly differently, some INI keywords changed, some added and a few taken away but with a lot of the core engine remaining in there and unused. With modules, what that looks like is that the garrison contain module for example may still be there but it will work differently and in a manner that fits the requirements of this game rather than a previous one - if what youre asking for is complete and total backwards compatibility then it probably wont happen as this is not a development objective, the objective is to code the engine and use it in a manner that will deliver the best possible LOTR experience within the SAGE environment. However, given the modular structure and object-oriented approach which is used, a high degree of backwards compatibility will be possible, although at alpha stage it cannot be clear just how much 'residue' (for lack of a better phrase) will remain, nor iis it entirely clear what will happen in future
The other thing to note is that a lot of things will be possible that may not ordinarily be used in the game - for exmaple some effects will be necessary simply to create the cinematic sequences - although those effects will be present and usable, they might not get used in gameplay itself.
Honest answers, hope they help!