Umpire over ball
 

I was at the WSU/CU game yesterday, and often the U would come up and stand over the ball after the RFP. With the timing rule change a couple of years ago, i.e. 40 sec play clock, the play clock is already running. WSU runs a no huddle, and the U standing over the ball halts the offense. Occasionally the play clock would get dangerously low. Why is the U standing there after the RFP? Is there some new mechanic/rule?

I didn't see the game but my guess is the offense made substitutions. When that happens, they must allow the defense an opportunity to counter those substitutions, so the umpire stands over the ball so they cannot snap it.

I'd also guess it was due to offensive substitution... the U stands over the ball to give the defense a match-up opportunity.

The rule says that the defense must not delay in making their match-up substitutions; however, if the play clock expires during this match-up opportunity, it's a Delay-of-Game foul on the offense (they should've made their substitution earlier).

Exactly correct. Teams in hurry-ups that try to sub after the ball has been placed do not like this but the rule was put in for a reason. Either get your subs in before the ball is getting placed or don't sub. These teams are usually not getting close to the play clock running out though.

Is allowing "the defense an opportunity to counter those substitutions" a new NCAA thing, or is this mechanic (having the U over the ball) new?

And how long does the U remain over the ball? Say there is a substitution with 10 seconds remaining on the clock, does the U remain over the ball for 2 seconds? 3?

As for "teams are usually not getting close to the play clock running out", I can't say that about WSU. It's been happening all season. My fellow fans (I'm a season ticket holder) know I'm a high school official, and frequently ask me questions. The U standing over the ball after the RFP isn't an NFHS mechanic, and this is the first year I've seen it at the NCAA level. (Edit: WSU is not a good team. The fact that it is struggling to complete substitutions is just one of the problems.)

I've seen this at the NCAA level for more than at least this year:

Rule 3, Section 5, Article 2

e. While in the process of substitution or simulated substitution, Team A is prohibited from rushing quickly to the line of scrimmage with the obvious attempt of creating a defensive disadvantage. If the ball is ready for play, the game officials will not permit the ball to be snapped until Team B has placed substitutes in position and replaced players have left the field of play. Team B must react promptly with its substitutes.

PENALTY—(First Offense)—Dead-ball foul. Delay of game on Team B for not completing its substitutions promptly, or delay of game on Team A for causing the play clock to expire. Five yards from the succeeding spot [S21]. The referee will then notify the head coach that any further use of this tactic will result in an unsportsmanlike conduct foul.

PENALTY—(Second or more offense)—Dead-ball foul, unsportsmanlike conduct. An official will sound his whistle immediately. 15 yards from the succeeding spot [S27].

I believe last season was the first year but not positive.

The Referee signals when the umpire is to move to the ball and when to move off the ball. If you are watching on TV, you'll not be able to see what the R is doing. Gotta be at a game to see. I see this because I'm now a timer... and yep.. team-A better complete their substitution quick enought for team-B to react else that play clock is going to expire.
Haven't seen that yet this year.. but it's been close.

During routine plays, I stand over the ball until the RFP blows.

During late game situations when a team may be in hurry up, I stand over the ball until the R is ready, I tell the snapper not to snap the ball until after the whistle and I back up.