You didn't ask me, but perhaps the following will help. I don't see any real point in commenting on alleged "mistakes" in the J3 case, but I can tell you what is different from a legal perspective.
In the J3 cases, the main concern was validity of the patents, and, although the PTO review was certainly a part of that, the J3 attorneys had raised the issue of validity in the litigation itself. In other words, regardless of PTO review, validity would have been put before the jury at trial and would have been decided by a group of laymen. Thus, in addition to the fact that Roger Cook and his firm were being paid by the hour (by recollection, corrections welcome, they were paid some $17 million by the conclusion of those cases), settlement was felt to be the preferred route even though we had was was believed to be a highly favorable Markman ruling from Judge Ward --- of course, the Markman ruling mainly affects infringement, not validity.
By contrast, the current T3 cases are pretty much the opposite. The PTO process is now apparently complete, so that validity is not as much of a concern as in the J3 cases. However, we have no Markman ruling in the current litigation, and, while Judge Ward's ruling from the J3 case is persuasive, it is not binding in California. As a result, and since the T3 cannot realistically put much hope in arguing validity, they are going with non-infringement --- which is the basis of the motions for summary judgment that have now been filed.
Remember, lawyers are paid to win if they can. I have posted this before, but the old saying is that when the law isn't favorable, you argue the facts; when the facts aren't favorable, you argue the law; and when neither are favorable, you just argue. That's how it works in litigation, and it ain't ever gonna change --- you go with what you got and you do the best you can, and lawyers practicing at this level can always come up with an argument that at least sounds persuasive.
Hope this is helpful as an overview. Best wishes.
