It's kinda dumb having this many NPC's and only end up using 3 or 4.
It's kinda dumb at 99 but if you use them as intended (help in leveling up now that no one really is leveling up) you will easily use 6 or more. Going into Crawler's Nest on 34RNG to do page 1 was tough but fast exp. I used Shan/Aji/Kupi at first for fast kills but their MP would run out before their timers were up or they'd come too close to dying. Solution was to use 2 teams: Shan/Val/Kupi, Aji/Mihli/Trion. Alternated those after every fight or two and was awesome. Some of those you need Rank 6 of course to get so they're intended for 65+ leveling but the older tanks/dd could be used instead. If I was 50+ I would have used Exc/Curi instead of Val at times to avoid AoEs.
I think it's handy to look at all the melee and chunk them into magic, melee, and tank with sub-sections of AoE, Non-AoE, and utility.
Magic:
Shan/Aji/Mihli/Kupi/Joa
AoE:
Mihili
Utility:
Joa/Kupi/Mihli/Aji
Melee:
Aya/Naji/Lion/Nana/Ten/Volk/Zeid
AoE:
Lion/Nana
Utility:
Naji/Volk/Zeid
Tank:
Cur/Exc/Tri/Val
AoE:
Val
Utility:
Tri/Exc
If you want AoE use bring one or more of Nana/Lion/Val/Mihli.
If you don't want AoE then you would use the others.
If you want magic damage use Shan/Aji otherwise use the others. Zeid is sort of a middle ground being melee with spells, works best if you need additional debuffing.
If you're focused on melee and don't need dedicated heals bring Joa; bring Aji if you're focused on magic.
If you need dedicated healing Kupi/Mihli but not Mihli if you don't want AoE.
If you would like someone to have higher enmity but don't need a dedicated tank then you would use Naji/Volker.
If you need a dedicated super tank use Tri/Val otherwise Exc/Cur will work. If you don't care about tank's damage output use Tri for stuns.
Another thing to look at is weapon type. If you'll be fighting a lot of birds or bees you might get more mileage out of Nana/Exc.
Looking at it like this, every trust companion has its uses. Except for maybe Curilla who just seems to be outclassed by the others flat out.
Otherwise for the future I'll probably look at these as any other spell, do you cast minuet 1 and 2 much after you learn 4 and 5? They're bound to bring direct upgrades over what we have at some point.