TY for the question! No current plans but I do have some thoughts...

For Engie and the other mercs I feel like Insight wouldn't fit too well. They're already loaded with customizable perks and items for fun. Too many layers on a cake.
I do think MvM's upgrades would make for an easy entry point into skill trees, I'd go that direction.
If anyone wants to discuss potential skilltrees feel free to though!

for Reign of Runts, however, I am interested in eventually exploring with Insight. They're more canon compliant so I think it'd fit them well.

and for the Shipwrecked Characters I likely just wouldn't want to. But on Island Adventures we may give it a try one day.

Overall? I think I'll wait to see how Klei continues to handle it as they add it to more characters before acting, still early to call.

I think you could reduce the amount of special things each mercs have and add in the skill tree instead. Working for a buff makes it more satisfying, and also give a higher level of customisation.

It could be in the form of MvM upgrades or item effects. Items effects in tf2 is already a kind of skill tree since you have to pick a loadout of your choice while foregoing the rest, and it require work to unlock most items.
Looking forward to the RoRs characters though.

Have his still tree background look like the MvM upgrade station
Reduce his speed penalty when moving buildings
Add the larger dispenser range and two-way teleporters
Add the ability to craft weapons like the Southern Hospitality, Gunslinger, and Wrangler.
Give the dispenser the ability to generate booster shots
Give a small speed boost when leaving a teleporter

Gunslinger

When equipped gain 25 more health
Removes the Less damage penalty
Deals 45 damage while equipped
Swinging animation is replaced with the punching animation
Every Third hit does double the damage
Grants the ability to craft mini-sentries
Mini-sentries will be cheaper to make and refill however will deal less damage and have less health
Mini-sentries can't be upgraded
All normal sentries will be destroyed when equipping the Gunslinger and vice versa when equipping a Wrench
Mini-sentries are more likely to be targeted
Every kill from a mini-sentry will be tailed as revenge crits in the corner of the gunslinger Icon (Can only store up to 35 revenge crits)
When a mini-sentry gets destroyed revenge crits will activate giving the user double damage. When the revenge crit counter reaches zero revenge crit deactivates
Each hit against an enemy with the Gunslinger depletes 1 revenge crit.
Dying loses all revenge crits