I think it's basically as complete as it can be, barring the remaining issues discussed in this topic that can't really be helped. It's cool to see this is finally done, nice work ShadowOne333! I'll stick with the SNES version myself after witnessing all the issues in the GBA port that likely can't be fixed, but for GBA fans this should do nicely alongside the sound effect hack.
Link to the Past GBA's palettes weren't actually too bad at the darkest setting. There are still inconsistencies but it's not the most offensive port visually. At least a brightness setting was included, and it might even make work fixing it easier. Some dark areas suffered a lot though, particularly the beginning scenes (inside Uncle's home before the lights come on as well as outside in the storm). Darker areas of dungeons were also too bright. I wonder if these can actually be fixed, Yoshi's Island had similar dark areas that couldn't.
There used to be a palette restoration for Breath of Fire, but i'm sad to say that I lost it and can't find any working links. The author Asaki (who did the palette restorations for Mario World and Mario 2) hasn't been online in years. The GBA port has a more intuitive user interface and multiplied EXP and gold to speed up grinding. Though the music was also downgraded. Some people seem to think it would be "easy" to recreate the palette restoration for the first game, don't know how easy though-http://www.romhacking.net/forum/index.php?topic=14142.0
BoF2 GBA has a palette hack which is still available, though I don't really bother ever since the fantastic SNES retranslation was released.
There are some "ports" that aren't worth messing with due to ruining well beyond palette and sound quality. Tales of Phantasia, Earthworm Jim 1/2 and the DKC trilogy for example. They're such sad disappointing messes overall that really get me down...
Some of Capcom's titles following the GBA's launch began to include brightness options to mostly get them looking like their originally did. Earlier games however are overly bright with no way to darken them. Disney's The Magical Quest was a good example that might be worth looking at. Super Ghouls and Ghosts also suffered a palette brightening, but good luck trying to play through such a difficult game to ensure everything looks right lol! Megaman and Bass however actually looks pretty comparable to the SNES version from what I can tell. And the two Magical Quest sequels had options to darken the visuals.
There is an ongoing translation project for Mother 2 GBA, seemingly with some good progress being made (48% as of the most recent August update on their facebook page). So taking a look at its palette could be worth it. Though the game also desperately needs a sound restoration as well (seemingly not many people know how to do this other than Bregalad). Though I do think it could be restored to its original SNES glory with some work. It doesn't seem to have many (if any) downgrades outside of the palette and sound (which could be fixed).