In my opinion, the move to a 35-man limit in 2007 was misguided and unfortunate. The product of the lone mid-major coach on the committee, it was intended to prevent the major programs from loading up on talented players to the detriment of mid-majors. In effect, the rule was expected to create a "trickle down" effect within Division I.
However, it seems to have had the unintended effect of funneling a disproportionate number of players to the JUCO ranks. After all, JUCO transfers need not sit out a year, and they become eligible for the next draft; unlike those who transfer within Division I. As a result, the rule doesn't seem to have met its proponent's objective.
Meanwhile, Division I coaches have been stripped of any latitude they might have had in the past to retain a few players who were at the margin of making the roster. Before the imposition of the 35-man rule, it wasn't unusual to see rosters end up in the neighborhood of 35-40 players. Now, coaches have no choice but to pare down to the 35-player figure before the beginning of each regular season.Then, to add insult to injury, they're prevented from taking back a previously released player in the event that a "counted" player is lost for the season.
Of course, not all players want to hang around if it's evident that they are considered to be on the roster cusp. However, there have been plenty of players in the past who would have preferred to remain on their original school's roster for any number of baseball and/or non-baseball-related reasons.
It seems to me that if the NCAA had simply imposed the 25% minimum scholarship/27 players-on-scholarship rule, roster sizes would have pretty well taken care of themselves. Some players not making it into the 27-scholarship category would have voted with their feet and transferred, while some would have stayed on as athletic walk-ons; fully cognizant of the implications. If this had been done, I think the results would have been much more satisfactory for players and coaches, alike.
(Ironically, the mid-major coach who pressed for the 35-player limit was subsequently relieved of his responsibilities after his players pulled off a virtual mutiny. What a legacy.)