I think it's legitimate to have some concerns right now. On the face of it, Lynch doesn't particularly fit our 3-4 system perfectly.
However, I think we should also expect that he's going to be more of a playmaker that doesn't simply rush the passer all the time. In other words, after his freshman season (in which we will probably see a lot of him strictly coming off the edge or going after the quarterback) he's going to be making plays in stopping the run, eating up blockers, and getting out in space at times and being disruptive.
I think we see Johnson and KLM and we like that they are good at taking on blockers, but neither have good/great pass rushing skills, at least that we've seen. Lynch seems like the kind of talent that is going to be bringing both facets to the table and that is a great thing to think about right now.
I think we also look at EJ and KLM and with them both at or close to 300 pounds and think all of our defensive linemen are going to be that size. I would suggest the coaching staff realizes their limitations as pass rushers (EJ more than KLM) and thought it wise to bulk them up as much as possible without losing speed, so they are effective at controlling their gaps.
But I don't think that means Lynch and other DE's we recruit in the future are going to be like that. In fact, I'd venture to say the coaching staff would prefer having a set of big space eating defensive ends, and another set of more athletic/pass rushing defensive ends. That gives them a ton of flexibility and is basically what has us drooling right now, right? So, we'll probably see Tuitt and possibly Sprigmann be the ones who are inching closer to 285-290 as youngsters, while Lynch and possibly Niklas are going to be 265-270 as youngsters, but likely never going over 280 or 285.
You see a lot of elite NFL Defensive End's around 270, so I would say since we run a 3-4 and want a little more bulk with our players at that position, but we won't see Lynch get too big. He's already gained 15 pounds and is at 260, I would say there's a good chance he never gets over 275 (which is the weight Justin Tuck plays at in the NFL) in his time at Notre Dame. I know a lot of people think he's skinny, but I think he's pretty well filled out already for someone his age. I also think that perception has to do with, again, seeing our older DE's who are just mammoth's right now.
So, valid concerns, but I think Lynch stays relatively "light" in comparison to EJ and KLM but brings so much playmaking ability to the table that he will be a force and able to play every down after his freshman year.