Where were you during the 2000s? It may not have been "win at all costs" (as there was not consistent winning) but discipline was breaking down all over the place. That staff was losing their ability to keep the team in line and their decisions were getting kind of bizarre. (I.e., playing guys facing assault charges while benching someone half a season for a prank phone call.)
I was watching and my memories don't conflict with my opinion in this thread.
I don't know your age, memories, or critical thinking abilities, but I remember:
a) a recruiting strategy twice in flux. If the recruiting gurus were
to be believed, the program was in the running for many national recruits, including the QB Simms and a number of NFL prospects who left us at the altar for whatever reason. Their plan Bs at many positions were major multiple steps backward. Again if I remember correctly, that was when Joe re-emphasized recruiting regionally within a 200 mile radius of State College
b) as far as athlete misconduct, Rashard Casey was not only found innocent, but receiving a substantial financial settlement over the situation.
I remember few or anyone who sided with Paterno for his support of Rashard (against charges from what proved to be wife-cheating off duty policeman) and fewer questions from the press when he read Rashard's thank you note in his weekly press conference
I think the LB Connor (if that is who you are referring) recovered to be in the top 5 for career tackles. In my opinion, but maybe not yours, crank calls to a coach aren't the acts of a team leader.
Joe (over-)disciplined and publicly chewed out many in his tenure. I particularly remember his year suspension of Bobby Engram, sorry not from the 2000s, for 'borrowing' a teammate's stereo. I don't know but would think Engram eventually appreciated this tough love, maybe as much as Michael Robinson did in his painful Penn State career where Joe predicted he would be an NFL All-Pro as a secondary position.
I wonder if the current team's bounce back would have been quicker had their coach had the courage (I believe Joe would have had) to bench Hackenberg for at least a few series.
Even with these issues, they still had 2 very good teams and were on a possible Big 10 conference championship game his last year.
Everyone has their opinions, memories, and values; feel free to express yours. I value recalling the team's journey from my being a Pitt fan but a Penn State student in the lat 70s through the pretty glorious 80s (especially when I look at the piece of goal post I have from the 83 Pitt game), and even the uneven 90s and 2000s.