Everything the original had, X@COM will have, assuming there's enough support for the project in the long run*.
*If very few people are interested, I'll probably discontinue development, though hopefully at least make some contributions for 3D RL environment implementation techniques in the process. Obviously way too early to make a decision on that--have to put enough together so people can at least understand my vision
I won't be making too many changes to the original for 1.0, only necessary fixes and interface functionality improvements. The only major change to the original game, initially, will be gravity and falling objects! Regarding UFOPaedia, I would definitely make it a little more helpful. For example: Damage for incendiary weapons should be shown correctly/differently. I was thinking of using ASCII graphics to show actual pictures of the objects/aliens/ships/etc. That's definitely for last, though (or at least after the geoscape dev has begun). For now the first major milestone is to get a fully operational battlescape with the full range of randomly generated maps and scenarios, so that people can get to killing aliens (initially with preset or random soldiers--basically a quick skirmish mode for X-COM).