Personally, my opinion is that the 2009 edition was much better than the re-release. Yes, The Second Coming Edition added a bunch of new content - locations, NPCs, quests and slightly tweaked the graphics. And yes, they added gamepad support. That’s essentially all the advantages of the game, if some of these can be called nth.
Well, what's with the optimization? But with it, everything is just bad. There are slippages, drawdowns, freezes... Either from the number of NPCs on the map, or from the updated textures, the engine does not cope well with updated textures. Some points were noticed with the fall of the main character behind the geodata, I thought such a bug could only happen in Skyrim. Or, a bug with the HP of the main character and the NPC. Bonetown, published in 2009, is a very hardcore game, it was very difficult to complete. But The Second Coming Edition became three times more difficult, since it became not at all friendly to the player (and this , not just my opinion). In the original game it was possible to use the console with cheat codes in completely hopeless situations, but in the re-release the console does not work.
In general, in order not to spoil the nervous system and play comfortably, it is better to play the original BoneTown from 2009, and this edition is still a raw, broken and unoptimized raw material.