3 centre halves (if you want to pigeon hole Toti as one, I think he's better than that personally) is fine as long as it's coached well. It doesn't have to be stodgy or restrict attacking progress, as O'Neil and others who play in a similar shape have proven. The way we play currently it means we get more bodies into forward areas than we would if we built with a more rigid back 4.
The biggest issues for us come from the way we defend with the ball, we often push 1 central midfielder into the forward line, the left sided WB central and the right sided WB high on the touchline. When we lose the ball there are spaces absolutely everywhere and apart from Toti and Semedo (as previously stated often pushed too high to affect anything at this stage) none of our defensive personnel are particularly strong when they've been turned. The first Newcastle (A) goal is a perfect example of this.
There's also that moment in transition where Toti is caught between LB & LCH. West Ham absolutely hammered us with that one. Poor guy was twisted up all game and came away from it looking dreadful but it was through no fault of his own really, he was let down by the system that day.
When we defend deep we actually do it very well, the extra 'centre half' playing as a LB is a huge advantage and with the pace we have on the break when Cunha/Hwang/Neto are available it keeps most teams honest. The only real issues we've had with it have been the extra defensive responsibilities placed on whoever is playing the right sided attacking role. Bellegarde really struggled with it earlier in the season and there's been a number of occasions where the RW has switched off from a throw in on that side and allowed a chance (The Man United & Coventry winners being the most costly).
A lot of Kilman, Dawson & Bueno's worst moments this season have come as a result of these weaknesses IMO. They've looked worse than they are at times (they're still not good enough individually). They've had to do a lot of 'panic' defending where a mistake they've made may have been the direct result of a goal but the root cause is the flaw in the shape which has put them in a disadvantageous position.
O'Neil has always talked like he'd like to be more tactically flexible than he's been allowed to be this season so with a hopefully more balanced squad (don't fuck this summer up Fosun) I don't think we'll see the 3-4-3/4-4-2 hybrid as much next season but we'd be foolish to ditch it altogether. It just needs to be coached better and hopefully with a full pre season O'Neil can get more of his ideas across.
Oh, and if you don't like 3 'centre halves' wait until we line up with 4 next season.
Mosquera - Kilman - Dawson - Toti
It's coming. What was it our idiot Twitter fans used to call Nuno? Portuguese Pulis?