I'll be doing some film work on Jim O'Neil's in the dull part of the offseason, but this article explains well what I've seen so far. It's been posted in other threads, and it also belongs here:
http://www.ninersnation.com/2016/5/1/11548550/the-49ers-off-season-so-far-reading-between-the-lines
Below are the relevant snippets from the article that speak directly to JoN's scheme:
O'Neil is an acolyte of the (Rex) Ryan tree. The philosophy and coaching pedigree are different (than Fangio). O'Neil was first coached by Pettine's dad in high school, then remained a good soldier for Pettine under Rex Ryan and followed him to the Bills and Browns. He's a field general, which is the perfect temperament for working under Chip Kelly but, by the same token, I doubt O'Neil would ever actually tinker with the approach he learned under the Pettine/Ryan philosophy. It's what he knows.
Under that "46" philosophy the guiding principle is to aggressively overwhelm the offense with pressure from numbers. Originally six men lined up at of near the line (4 DL, two LB) and two more stood just behind (SS and MLB).
For a Cover One shell to work in a Ryan defense one needs (a) exceptional man corners who can press and (b) some unpredictability about who is actually going to rush the passer and who is going to cover who. No doubt influenced by LeBeau's zone blitz concepts, modern versions of the Ryan defense utilize two main elements to accomplish this goal: hybrid defenders that line up all over the place and play different roles from play to play, and at least one really good corner on an island. At the Jets, Pettine had Darelle Revis. In Cleveland O'Neil had Joe Haden his first year. With Haden, the Browns were a top six defense against the pass
If I had to draw a comparison that all 49er fans know, it's that JoN's scheme is very much like what we've been seeing from ARI over the past few seasons. Crowd the LoS, confuse pass protection, man up on the WRs, lots of blitz packages.
For recent comparisons, Fangio operated out of a Quarters look with two safeties back while running complicated pattern match concepts, rooted in man concepts. Defensive fronts were very static and he looked to confuse the QB by giving him the same presnap look down after down.
Mangini was rooted in zone concepts, while trying to cause confusion in pass protection by mixing up who the 4 pass rushers would be (ex: drop an OLB into coverage, rush an ILB).
JoN is a mix of these two in that he will give various looks to his defensive front, mix who the rushers will be, and bring pressure often - this part is like Mangini. He is rooted in man concepts - this part is Fangio, but he will not use complex pattern matching rules as Fangio. JoN plays some press, but more off coverage from what I've observed from his 2015 CLE team.
My guess is that he wants his blitz pressure to get home, while having his CBs watch the QB dropback. If the QB hurries and throws a pass because pressure got through, then the CBs are able to drive downhill and make a play.
One memorable play that I think fits what JoN envisions as the perfect outcome in his scheme is Bow's pick 6 at the Stick. CBs in off coverage reading the QB drop. Pressure gets through, drive on the throw. The defensive playcall here is Cover0, which is an all out blitz so it's a bit extreme, but the concept in play are right up JoN's alley. This is Fangio's defense, but we all know Fangio was not much of a blitzer.