In my opinion, multiple health bars is good final boss design. It prevents a single, massively overpowered unit from wrecking the final boss by itself. By ensuring that even the most busted unit can only kill one bar at a time, the boss remains on the field to pose a threat.
The other reason is system limitations. GBAFE has a hard HP cap of 127, so if you want the boss to last a good long while, the only way is to give it multiple healthbars. This isn’t too hard to do; just spawn another unit in upon the final boss’ death.
In terms of boss stats, I personally prefer an approach similar to FE12 Lunatic Medeus, though with some changes. On that difficulty, Medeus’ stats present every bit the threat he is made out to be over the course of the story. With 30 SPD, he doubles all but the fastest classes, and with 60 ATK, he 2HKO’s anything in the game, even Generals. 40 DEF makes even maxed units with Regalia deal single-digit damage, and the Falchion just 24 at max. The fight makes you feel very outclassed; the strongest mortals with the best weapons can barely scratch him, and that is what a final boss should be like when made out to be a threat much greater than what humans are capable of.
That being said, Medeus does take these stats too far in a regard. First, this is Lunatic difficulty, hence he’s supposed to be absurdly difficult. On Maniac, he’s almost as strong, though a bit more lenient on the SPD front, while Hard and Normal are pretty easy by comparison. Forcing the player into a narrow selection of 5-6 classes is not good game design.
As such, in regards to stat distribution, the final boss should feel imposing, without outright being near-impossible. It should have enough speed that most medium-speed classes (Hero, Paladin, Sage etc.) can’t double it even if capped, though do risk being doubled if they are lacking severely in speed. Slow classes (General, Wyvern Lord etc.) should always get doubled, but should be among the only classes capable of surviving two hits if bulky enough, as bulk is what slower units excel at anyways. Fast classes (Swordmaster, Falcoknight etc.) should be able to double the final boss by the skin of their teeth, as their lower STR caps limit their per-hit damage. As for durability, ideally “weak” classes should do about as much damage with two hits as “strong” classes do with one. As the difference in STR cap is 8 points at the greatest, you usually only want the final boss to take 6-10 damage from weaker classes per hit, hitting twice, while stronger classes can nuke the final boss for 16-24 damage at a time. Any well-trained unit with an S-rank weapon should be able to achieve this; everyone should have their fair shot of fighting the final boss if trained.
As these stats are mostly based off of class caps, some degree of insurance is needed in case the player walks up with a mostly-dead army and an undertrained Lord. It is the Gotoh’s job to prevent this. Whatever class the Gotoh is in, they should have stats at or near caps, or else have exceedingly high growths to ensure they reach these thresholds by killing enemies on the final map for EXP, which they should be able to without too much effort. They should start with an S-rank in something, enough stats to use that S-rank weapon competently against the final boss, or else have their own PRF to the same effect. This ensures that you will always have someone that can kill the final boss, though the Gotoh will still need healing support to do the job, and can’t do it as fast as a crew of 4-5 maxed units can. On that note, put some droppable Elixirs in the final map so the Gotoh won’t run out of healing before they can slowly chip the final boss to death.
As for the Lord and their Legendary Weapon designed to wreck the final boss, the Lord should be subjected to much of the same stat bracketing as other classes; they do not outclass the final boss on their own. The Legendary Weapon should enable the Lord to do more damage than anyone else can, but that’s it. It shouldn’t enable the Lord to take a 2nd hit (reserved for bulky classes) or double the final boss (reserved for fast classes), and, due to the presence of a Gotoh that can kill the final boss by themselves, if slowly, using the Lord and their Legendary Weapon to kill the final boss faster is a privilege, not a right. If your Lord is undertrained, then you must spend the extra time with the Gotoh doing the job. It should not instantly make the Lord competent at fighting the final boss; powerful weapons are as powerful as their wielder, and a wielder that dies in one round shouldn’t be very powerful due to it.