While I agree 3-4 will probably be the base, I don't agree with a large portion of your statement.
Ware was never a 3-4 linebacker until he came to Dallas. Spears was primarily a 4-3 end and was projected as a prototypical 3-4 end.
Also, if you read the recap of Parcell's press conference, he did say the nickel would be a 4 man front. Agreed. However, he also said he was trying to decide what percentage the rest of the defense would be. He seemed to allude that there would be 4 man fronts other than the nickel, he just hadn't decided on what percentage yet. Not 4-3, but 4 man fronts based off of the 3-4.
http://cowboyszone.com/forums/showthread.php?t=31759
I believe there have even been some 4 man fronts with Ware as a LB.
Now, this doesn't mean 4-3, but it does mean more 4 man fronts, which is a good thing. The most talent on the defense is on the DL (or the secondary, but not the LBers). Four man fronts will help get guys like Spears, Ellis, Canty, Ferguson and Glover on the field more.