Everyone has his own list of things that "well, imho it would work better like this" or "damn, this is silly, it should be different" or "I'd like to see this feature". Perhaps the most common wish is to have a larger party in order to avoid dropping valuable characters during the way, but unfortunately this is hardcoded. Other things are editable and both mods and the EE tried to add new features: for those who want to romance Nalia to those who want to bring Yoshimo to level 40 agaist Amelyssan while meeting new NPCs or locations meanwhile.
Which features did you want to see the first time you played the games? Even those that were later fixed by a mod or the EE, but you absolutely wanted to see during your first playthroughs.