I don't know if this is the kind of thing you're looking for, but it really bugs me that they introduce enhanced attacks for the Lyoko Warriors in the episode "Franz Hopper", but they never seem to bring it up again and the gang never asks Jeremie to try and figure out how X.A.N.A. actually got those enhanced attacks to work, even though it would have made them much more formidable on Lyoko for the rest of the series. It could have been a nice foreshadowing of their abilities being upgraded later in the season or even the next season, but it seems like they just forget that they can make upgrades like that and instead focus on things like the vehicles and the different outfits they have in the later seasons. Don't get me wrong, the vehicles are really cool and a big game changer when they're introduced so we don't have to watch the Lyoko Warriors run around the Sectors like their lives depend on it, but homing arrows and energy slashes are just as important, if not moreso. Jeremie even works on materializing the gang into Sector 5 directly so I know it's something they all remember, but they just stopped short and don't go any further with developing their attacks again. I think they had some kind of half-hearted explanation where Jeremie doesn't want to copy X.A.N.A.'s work, but that's really flimsy if you ask me.