If the "very mundane skill effects" are critical, they are worth sinking points into, provided player has enough points left. I would put 10 in Fleet Logistics if I have enough AP/SP left. (I do not unless I cheat and give myself a level in the upper 50's) Aside from Logistics, +OP%, and combat speed, I put points in skills with the best perks and/or hullmods.
- reward the player with something meaningful & visceral
+5% missile speed/rank
+10% target leading for autofiring weapons/rank
+1% flux capacity/rank
+1% flux dissipation/rank
etc etc
If I showed you 2 videos of battles, one with 100% flux capacity, the other 101% flux capacity, you'd be unable to discern which was which. (slight differences in the HUD not withstand)
What I'm suggesting is that all skill-ups should be meaningful & rewarding.
could you give an example skill tree? I know it's a lot of work but it would help immensely in conveying your idea.
Sure, here's the SOTS tech tree.
http://sots.rorschach.net/images/3/39/Techchart.jpgSure, it's got some boring stat-ups like Cybernetic Interfaces (+20% industrial output), or incremental stat boosts (missile, laser & armour techs), however the vast majority of them are far more visceral.
They either give you access to new weapon designs, new engine types, new ship hulls, new tactical components (shields, cloak, minefields, bio weapons, point defence).
I suppose Diablo 3 is an interesting example too.
While its skill system was much maligned for being too simplistic (to which I agree), it had the right idea about discarding the pointless 'filler' skills that dominated Diablo 2's skill tree.
e.g. levelling up your Mage's Blizzard skill from lvl 19 to lvl 20 so that your spell does 50 more damage is neither engaging, nor rewarding.
I don't think comparing a 4X tech tree to an RPG skill tree is particularly relevant.
SOTS was merely an example of a visceral advancement system; I don't think it matters if it's a character 'levelling up', or a civilization 'teching up', the need for the advancement to be engaging & rewarding transcends genre boundaries.