Not sure I understand this. On the Patriots website Jones/Ninkovich are both listed as DEs. Patriots play a hybrid, correct?
Every defense should probably be considered multiple now, yes. The Patriots decided their best front had Jones at 5-technique during the preseason, with Hightower and Ninkovich as OLB and Collins and Mayo inside. They were already experimenting with ways to move Jones around in the last weeks of the preseason and early weeks of the regular season. After Mayo's injury and the struggles with player depth along the line, they began standing Jones up more as the season progressed. After he returned from his hip injury, Jones was almost exclusively a standup linebacker. Ninkovich played the majority of his snaps from a two point stance all season.
In recent seasons, the Pats had leaned heavily 4-3 -- so that's how Rotoworld had them through the preseason. By the time it was more clear the Patriots would approach 2014 differently, it was past the time when MFL made positional changes. I don't use RW depth charts expect when I do tiers, so I don't know when their charts moved those two players from DE to LB.
The team websites are not official charts and aren't much help. The gamebooks are also messy. They list three defensive tackles with Jones and Ninkovich at DE a number of times last year.
This is not set in stone at all.
If Mayo is healthy, the Patriots will look at Hightower, Jones, Ninkovich, Easley and a couple of other rotational linemen and decide how to best use them. I think there's a good chance we see Jones at RDE and Ninkovich and Hightower as 3-4 OLB again to get both Mayo and Collins on the field inside. For now, Jones and Ninkovich are listed at LB on MFL. I'll note all this in the blurbs that accompany these players in the tiers. In fact, for clarity's sake, I may put an entire sidebar together on this situation.