It's been a while, but I just wanted to follow up on this since it is something which I still consider a problem. That being said, I have made some improvements that are really helping that I wanted to share.
For starters, I have read everything on this forum on this subject as well as others, and I will say that in my opinion there isn't one solution which really solves the problem completely. If you're looking for a complete and total one-stop fix, I'm afraid to say that it probably doesn't exist.
That being said, all of the suggestions people have made combined (including manual control) do really make the game much more enjoyable, even against the worst spammers. The big thing though that nobody has really clearly stated previously, but which may just be my opinion is simply the importance of speed in the back line. After growing frustrated with none of the suggestions really working as well as I had hoped, I went and took a look at things myself by saving numerous through-ball/breakaways and watching them in slo mo in the instant replay gallery. What I noticed actually surprised me. I had thought that the problem was more a case of defenders being in poor positions, but in the majority of replays I was shocked to see that the defender was actually starting in a normal, or even excellent position when the throughball was played. So, in all these cases it was a matter of asking, "why, in god's name, would any striker latch onto a ball played like that when the defender is in the proper position?!!?!"
The answer isn't 100% clear however. I noticed in some cases that the defending AI seemed to take a long time to turn from facing the ball to running to catch the striker (who by that time was miles ahead of them). In other cases I could see a small glitch in the movement of the defender, as if they stopped for a moment to tie their shoelaces, and let the striker blow past them and be free on goal. This might be just due to player switching, but my point is that all the talk about the defensive line being too high is not 100% correct in my view now. In fact, I'm playing with a deep defensive line (0) and pretty smart defenders, and I can say that I believe that positioning isn't the biggest part of the issue, or at least it isn't the ENTIRE issue.
All this being said, when I watched all these replays I started to notice that in almost all of the cases I said to myself that "speed would help." That's not to say that the problem is necessarily the lack of speed of the defenders, but rather that IF your defenders were fast enough, it might really help. So, I bit the bullet and purchased Perea, then several other defenders with 85 or more for top speed. I also tried to buy defenders who have high explosive power and responsiveness. I'm not sure if explosive power (acceleration) would help, but I thought it couldn't hurt since it is really essentially a problem of not being able to turn and accelerate quickly enough (regardless, most defenders don't have very high explosive power, but I'm just saying that I stayed away from those with lower than 75 if possible). Responsiveness too helps, but after this little adjustment to my MLO squad I can say that there certainly is a big improvement. If nothing else I can name several times when Perea of others have literally outpaced Vand Der Mirch or Eto and stopped a certain goal, and that is certainly something I had never been able to achieve prior to this change.
Anyway, it's just something I wanted to share because I don't think it has been stated very clearly in the past. Others have said "buy fast defenders" but for me anyway I like to understand why that is, and what the actual problem is, which I feel like I understand better now.
Note however that once you switch to fast defenders there is generally a trade off in their defensive awareness, because the likes of Perea for example have only 75 or so for def awareness. This translates into a noticeable downgrade in tackling ability in the back, which for me at first meant that I was unable to tackle players making mazy runs in the box who previously I would have been able to strip the ball off of quite easily. I've rectified this for the most part however by having tough-tackling sidebacks, like Vermaelen or Dunne (not true side backs, but you can see why I use them I think). This is especially helpful because most of the dribbling comes from out on the wings, but also because these SBs have high df awareness and will help in the middle of the pitch when needed as well.
Anyway, I hope this helps, and good luck with those spammers