The problem with all but four of the players you listed (Bay, Thome, Bonds, Stubbs) were either a high school player when drafted or was an undrafted free agent.
And the four
Bay - a 22nd rounder, skipped rookie ball.
Bonds - Skipped Rookie ball - then Played half a year a A ball before going to AAA.
Thome might as well be a high schooler, as he was a draft and follow who played one year of JC ball before signing. But yes, he did struggle at 19 in his first season at Rookie Ball.
Stubbs - 1st rounder with a mediocre start in Rookie Ball.
Which is the exact point I was making earlier and johngalt elaborated on.
"Polished" college bats should be ripping the cover of the ball in rookie league if they get placed in that league at all if they want to have any future. Most are deemed above that level and can move on to higher competition.
For immediate comparison, the only other college bat taken in the top ten, Evan Longoria, tore up Advanced A ball and leveled out at AA.
Just to further hammer this home. Lets look back a few years just to let some history develop. These are the top College draftable bats of the year, taken in the 1st round of that year's draft.
2002 Draft 1st Round College Bats
Drew Meyer - Skipped Rookie Ball - Started off in Low A where he OPS'd 593 - and he's been awful ever since. A career AAAA player.
Khalil Greene - Skipped Rookie Ball - Put up an OPS of 893 in High A in his first year.
Russ Adams - Skipped Rookie Ball - OPS'd 933 for Low A in his first year
Nick Swisher - Skipped Rookie Ball - Started in Low A with an OPS of 888.
2003 Draft 1st round College Bats
Rickie Weeks - Played 1 game at Rookie ball before moving to Low A to OPS 1050
Michael Aubrey - Skipped Rookie ball and went straight to Low A where he OPS'd 960.
Aaron Hill - Skipped Rookie Ball and went straight to Low A where he OPS'd 938.
Brian Anderson - Played 13 games at Rookie ball (and OPSing 1084 in 58PA) before moving on to High A and put up an OPS of 925.
Brad Snyder - Skipped Rookie Ball and went straight to Low A where he put up an OPS of 860
Conor Jackson - Skipped Rookie Ball where he moved onto High A and OPS'd 943
2004 Draft 1st round College Bats
Stephen Drew - Sat out a year, but when he came back, he skipped Rookie Ball and started at High A where he put up an OPS of 1224
Josh Fields - Skipped Rookie Ball - Started off at High A where he put up an OPS of 778
Landon Powell - Skipped Rookie Ball - Started off in Low A where he put up an OPS of 725
Richard Robnett - Skipped Rookie Ball - Started in Low A where he put up an OPS of 841
I don't think OPS is the end all be all of hitting stats, but it's a quick and dirty way to show batting eye & power.
The only players on there who started off with a 1st season OPS under 800 (like Stubbs 768) was Drew Meyer, who pretty much can't hit at any level now going on four years. Landon Powell, who was a catcher and didn't start out on fire a full level above Stubbs, and Josh Fields, who didn't play baseball full time until he was drafted, but still put up the same numbers as Stubbs two full levels above him.
The Rest, all put up better numbers, and they did it against better competition at a higher level.
Do I really need to keep going? There are reams and reams of this out there that keeps constantly pointing at the same ending.
If you don't hit in rookie ball as a college bat, your future is pretty bleak.