I suspect that what many people have trouble with is that trees are inconsistent in what gameplay parts they affect.
Combat is easy, it's all just buffs to your flagship. If you want to buff your flagship, you put your points there.
All other trees are a mess. L1s buff your ships in general, L2s buff your officers, L3L buffs your ships and L3R buffs your carriers, L4s buff your officers, L5L buffs your colonies and has absolutely nothing to do with all the previous levels and L5R buffs your colony, your fleet and also has nothing to do with all previous choices.
T1s buff your fleet/campaign ability, T2s buff your flagship, T3s buff your ships, T4s buff your ships, T5s buff your ships.
L1s buff your fleet, L2s buff your flagship, L3s buff your fleet, L4L buffs your ships and L4R buffs your officers, L5s buff your colony (this time, at least some skills have relevancy to colonies, by making exploration easier).
So combat is 10/10 flagship buffs (with 1,5 carrier buffs).
Leadership is 4/10 ship buffs (1 carrier buff), 4/10 officer buffs and 2/10 colony buffs.
Technology is 6/10 ship buffs, 2/10 fleet buffs and 2/10 flagship buffs.
Industry is 1/10 ship buffs, 4/10 fleet buffs, 2/10 flagship buffs, 1/10 officer buffs and 2/10 colony buffs. If we assume all fleet skills are useful for exploration (thus also buffing colonies), then it's kinda-sorta 6/10 colony skills.
I think people expect Leadership to be focused on officers or carriers, and the latter it isn't really, the former it kinda is, but only if those officers use destroyers or, preferably, frigates. For cruiser or capital ship officers, Leadership is 2/10 officer buffs.
I wonder if swapping L1L/Weapon Drills and L1R/Strike Commander would make Leadership more palatable to critics.