Aright, so your Rotom is obviously going to be offensive and not defensive. Also, I am assuming this is in-game competitive battling for ORAS, since you want to keep the Nature. Going by that logic and the frailty of Mega Sceptile, your Rotom should function as a bulky attacker, with EVs invested in whatever stat your team is lacking in. Since you are running WoW, Rotom gets a pseudo-Defence boost, therefore the remaining EVs go into Special Attack, Special Defence, and HP.
EVs: 252 HP/108 SpA/148 SDef
(EDIT: if you want a basic spread, go 252 HP/252 SpA/4 SDef
- Hydro Pump
- Volt Switch/Pain Split/Light Screen/Reflect
With a Modest Nature Hydro Pump hits like a train. Discharge pairs well with Sceptile, but keep in mind that it may be a hinderance to your team once Sceptile goes down, but I'll get to that soon. Will-o-Wisp for Burns and a pseudo-Defence boost. The final slot is dependant on your preference. I removed Signal Beam because it isn't a great Doubles attack, if you want confusion go for Confuse Ray and if you want Bug coverage put X-Scissor or U-Turn on one of your other Pokés. Volt Switch gives Rotom a retreat option, a second Eletric STAB, and could form a VoltTurn core with another teammate. Pain Split keeps Rotom alive longer and weakens high-HP opponents for Sceptile to finish off. Light Screen and Reflect give some more protection for your team.
I hope my advice was useful and I hope you have much success in Doubles.