You make sure each choice is reasonable on its own and that the choice itself is meaningful.
The reason the FE8 vanilla split tree is awkward owes to two large reasons –
First, a lot of the choices have a no-duh on which one gives you more value due to weapon type access;
Second, a lot of the choices don’t matter because FE8 doesn’t challenge you on your tool choices.
When considering the Archer, whose options are Sniper and Ranger, gaining swords is a lot better than gaining stats. This is because while 1-2 is common, 1-1 is even more common.
If you’re looking at Pirate; Warrior’s 2 Skill and extra bulk is fairly helpful - though I totally agree it’s likely to not be as helpful as the extra Speed offered from Berserker.
If you’re looking at Fighter, then there’s also Warrior’s Con bonus to consider - but the non-Ross Fighter in the game is Garcia, who has insane Con and mediocre Speed, so Hero’s speed bonus is far better for him in particular.
And this is sort of where and why it all falls apart: Whether a class choice is useful heavily depends on the actual units that get those classes as well as the chapters they’re on, not just the classes themselves.
For example, Gerik does amazing work in Hero, due to having enough Skill and Con to use axes, and axes are incredibly powerful in FE8 due to enemies favoring quantity over quality, making killing many enemies in a turn a general positive and something fairly difficult when you don’t have 1-2 access due to the number of enemies that have it.
It’s not like he does bad in Ranger, and the gained weakness is basically nonextant because there’s so few enemies in FE8 that have effective weapons and even the ones that do don’t pose enough of a threat on their own. But the thing is that having the bonus movement, as amazing as it is, is not as productive in FE8 due to it having a large number of tightened maps, that aren’t absurdly oversized - you don’t spend multiple turns “just moving”.
(Also +2 move is ABSURD and Boots are, in most games, one-per-game. so getting a free boots at cost of a few other stats is FANTASTIC.)
So to answer the question in summary, you have to make sure that each choice is actually a choice. That can come in from multiple places.
For an easy and bad example, adding huge maps increases the value of movement.
… But if you have only huge maps, movement now is even moreso the most important stat
You can make each promotion offer a different weapon type, so that a different utility is gotten based on the choice.
… But that requires making sure that the weapon types are of actually equal value. Look at L’Arachel in FE8; there’s almost no Light-wielding enemies and tons of Dark-wielding ones so choosing Mage Knight basically gives you an instant -30 to -40 hit against all magic enemies, which might be significant. But Light tomes are heavier, so Valkyrie is slowed down - by 2 points, which can be huge.
… But overall, that’s all so minor that it’s a wash, because “2 speed or 30 hit” doesn’t matter when you have 20 speed against enemies with 10, and 140 hit against enemies with 20 avoid.