- some textures look bad/weird from distance (ground textures, some bush textures, etc)
Unit sprites aren't done yet (being done for the move to 1.5, from what I've gathered from these forums), other textures and such aren't because of EB. It might be the graphics settings that are at fault.

- lack of some details that add feeling realism (trails, blood, etc)
Hardcoded. Modders can't change this. There is a blood mod out there but it only works for missile weapons and looks pretty average.

- some animations are too stiff/unrealistic (skirmishers and those with javelins on horses)
Agreed, some of the animations are stiff. Equites, for example.

- unability to engage diplomacy with small tribes
Hardcoded. RTW has a limit of 21 factions, including Rebels (Eleutheroi in EB). The Eleutheroi are one of these factions, so engaging in diplomacy with a "small tribe" is like doing so with a single, big faction. EB has done some work on this by adding "alliances" that smaller cities have with larger factions, such as Kyprus being "allied" to the Ptolemies, but I don't think there's much else that can be done.

- sometimes weird AI behaviour in combat (sending his troops forward and backward for no appearant reason and such)
AI is hardcoded. The move to 1.5 might rectify some of the AI issues, though, such as advancing in cohesion.

- too weak aspect of troop morale in battlefield (low morale troops obeying totally idiotic orders, etc)
Good idea, but hardcoded. Unless someone can come up with a battle script where certain commands are greyed out when a unit has reached a specific morale level (which I doubt is even possible, without a ton of code), then it can't be touched.