Couldn't agree with you more.
You feel that way because that's exactly what is happening. The starting D-line is made up of guys recruited to and for the 4-3. The guys behind them were specifically brought in for the 3-4.
If you remember, prior to the 2013 season, the belief was that the D-line was going to be horrible. They ended up being much better than expected, but it's still the same guys. We are definitely in a transition period, between two defenses. We played a bunch of guys that were recruited for two different schemes this year. If you look at the DB's Mike Stoops has targeted since his arrival, they are different than guys like Hayes and Wilson. Not so much at the LB spot, since Evans and Alexander were brought in by Mike and Striker played in a 3-4 in high school.
I think that's been part of the problem with this year's defense (especially the secondary). Sadly, Mike couldn't figure out a way to make it work.