Actually, the primary gears (#4995) are new in the 2.5. This was a running change that was made in some of the newest generation one T-Maxxes, but all of the 2.5's have this change. Traxxas changed the way the forward and reverse primary gears join together, and they way that the gears attach to the primary gear shaft (#4993). The way the new gears join seems to be more durable. I have broken the old style in the past, so it was a need improvement.
Traxxas also changed the inner diameter of the brake hex (#4966x) to accommodate the increased diameter of the new heavy duty drive shafts.
To answer your question the FOC (#4994x) hasn't changed. It will work in both versions of the tranny. Traxxas did make a running change in the FOC, though. Several months back they changed the material for the gear in the FOC. The new and improved FOC's have a white gear as opposed to a blue gear in the old ones. The new gear is supposed to be more durable. The blue gears were prone to stripping under high power. If you can I would try and get the FOC with the white gear.