Like, is there a Skill to definitely level up I guess. I mean some skills are weapon boosts so if you have multiple people with that weapon you want to level it I guess.
It's been a long time since I maxed out the skill tree, so I don't remember what my progression was, but I don't recall it being very important to choose one over another. You'll eventually get them all, except for one choice at the bottom of the weapon tree where you can take only one of two options.
RyenSaotome speaking of the skill tree, once you maximize a skill, you can't see what it does any more.
I dug into the map files to pull this out:
Weapon Skills
- Bows (+3 atk w/ bows per skill level, affects Mirel)
- Daggers (+3 atk w/ daggers per skill level, effects Sandra and Vampire)
- Gloves (+3 atk w/ gloves per skill level, affects Brad)
- Guns (+3 atk w/ guns per skill level, affects Elly)
- Ice (Tsubaki gains Ice Slash and Blizzard Slash skills; cannot take Wind Skills)
- Katanas (+3 atk w/ katanas per skill level, affects Tsubaki)
- Maces (+3 atk w/ maces per skill level, affects Kayelinth)
- Magic Attack (+2 magic atk per party member per skill level, affects everyone)
- Spears (+3 atk w/ spears per skill level, affects Trey)
- Swords (+3 atk w/ swords per skill level, affects Ryen)
- Wind (Tsubaki gains Wind Slash and Hurricane Slash skills; cannot take Ice Skills)
Magic Skills
- Fire Magic (+50 fire dmg per skill level)
- Healing Magic (+50 HP healed w/ magic per skill level)
- Ice Magic (+75 ice dmg per skill level)
- Lightning Magic (+75 lightning dmg per skill level)
- Maximum MP (+30 maximum MP per party member per level)
Stats
- Agility (+3 agility per party member per skill level)
- Defense (+3 def per party member per skill level)
- Luck (+3 luck per party member per skill level)
- Maximum HP 1 (+50 maximum HP per party member per skill level)
- Maximum HP 2 (+100 maximum HP per party member per skill level)
- 3 skills remain grayed out for me, I'm pretty sure these cannot be unlocked yet:
- Critical Chance (+3% critical chance per party member per skill level)
- Evasion (+3% evasion chance per party member per skill level)
- Hit Chance (+3% hit chance per party member per skill level)
Other
- Build Cost (buildings cost 5% less per skill level*)
- Fast Learner (+300 XP per party member, can choose this an unlimited number of times)
- Lockpicking (+5 to Sandra's lockpicking skill per skill level)
- Mining speed (mines produce faster*†)
- Morale (+5 Army morale per skill level*)
- Potions (+100 HP healed per potion per skill level*)
- Presents (makes gifts more effective*†)
Some skills are prerequisites for others (like, you have to buy Max HP 1 before you can buy in Max HP 2). Most skills have 5 ranks, and you have to buy all 5 before you can buy any skills with that one as a prerequisite.
Skill Strategies
The Ice skills for Tsubaki give her powerful attacks that are defended by magic defense instead of physical defense, so those are worth investing in, which requires buying max ranks in Katana first. Ignore the Wind skills, Ice is more powerful than Wind: it gets bonus damage from the Ice Magic skill (up to +375), and the Wind skills have no bonus damage. The rest of the weapon skills are less valuable, because each character can only use a single weapon type, and the only characters that use the same weapon type are Sandra and Vampire, so each rank buys a small increase to one character (except daggers, which helps 2 characters, and maybe magic attack).
The Fire, Ice, and Lightning skills are also big powerups for Chiyo (and Ice also benefits Tsubaki). Healing is great for Mira if you have trouble keeping your party members alive, but I'd save that for later otherwise.
Stats are probably worth saving for later too. These will help keep the party alive, vs making enemies dead via the weapon skills.
In the Other category, the only skill I would consider mandatory is Lockpicking, which will help when you encounter a few locked doors and chests throughout the game which otherwise would block your progress or hide some treasure - I think that one of the quests that you need it for is a main quest, but I could be wrong about that. Build cost might be worth investing in depending on how it is implemented. If it just reduces the building cost in gold, then don't bother. If it reduces costs in other materials, then it might be worth it if your supply/production of wood/stone/etc is so low that you have trouble paying for buildings.
Stay away from Fast Learner until you have no other skills that you can buy (and you'll probably want to keep 15 skill points banked for the 3 skills that can't be unlocked yet). All it does is add 300 xp to each party member, which is basically nothing once you get to the point in the game where you can afford this.
If Tsubaki, Chiyo, and/or Mira are main party members for you, then invest in their skills first. Otherwise, invest in weapon skills for your main party members if offence is your biggest problem, or stats if defense is your biggest problem. You can put off investing in lockpicking...until you want to open some chests and doors. If you put it off, you might get blocked at some point and have to set aside a quest or note the location of a treasure chest to return to when you get Sandra's lockpicking skill up.
* I'm not certain whether or not these skills have actually been implemented, and I don't feel like digging through the map files to figure them out.
† I don't know what numerical effects these are supposed to have. I could not find any references to them in the map files.