I just used your team for a couple battles, since you gave us the text for it.
So far I've only came across two issues. The first has already been mentioned, Drain Punch works much better on Scrafty, especially since it's paired with the life orb.
My second issue is probably just me... but I've come across numberous Swampert Leads... and Rotom can't do a thing, and is forced to switch. I'm tempted to swap out HP Fire for something.
I've never used Latios in my life... and I'm loving it.