A couple of disclaimers first:
1) I've been absent from SO for a while, so I don't know if this subject's been addressed already; if so, I apologize for the redundancy.
2) These suggestions for a cast were not my original idea; in fact I haven't heard of these actors before, though some of the faces are familiar. I was looking up something from a GI blog, and ran across this: I looked up the actors and thought, yeah, he would be a good professor, or she'd make a great Ginger, or Skipper, etc. So here goes. See if you agree. I'm sure most of you are more familiar with these people than I am:

Stephen Colbert (other than Colbert, I don't know the others) as the Professor; 
Isla Fisher as Mary Ann;
 Seth Rogen as Skipper (he doesn’t have to be old)
Eugene Levy and Catherine O’Hara as Mr. and Mrs. Howell; 
Christina Hendricks as Ginger; 
Christopher Mintz-Plasse as Gilligan

First, welcome back!
Second, it was kind of discussed back when the movie was first announced, but no one's brought it up in a while. So on that note...

If someone doesn't cast Simon Baker as the Professor in the new movie, a casting director needs to get fired. And Christina Hendricks possibly as Ginger - she certainly looks the part. I don't have strong choices for the others yet, but Holland Taylor would be a super cute Lovey Howell.

First, welcome back!
Second, it was kind of discussed back when the movie was first announced, but no one's brought it up in a while. So on that note...

If someone doesn't cast Simon Baker as the Professor in the new movie, a casting director needs to get fired. And Christina Hendricks possibly as Ginger - she certainly looks the part. I don't have strong choices for the others yet, but Holland Taylor would be a super cute Lovey Howell.

First, thanks for the welcome back. I looked up Simon Baker. I agree; you are EXACTLY right on! A very strong likeness to the Professor.

A friend of mine suggested a young actor called Jason Dolley, from a Disney Channel show called Good Luck Charlie. She thinks he'd make a good Gilligan.

The toughest character to replace, I always believed would be Mrs. Howell. Natalie was a very unique actress. The easiest I believe would be Ginger. There are so many Gingers trying to break into the movies. I don't know if Helen Mirren would be too old to play Mrs. Howell. I believe she could pull it off well. I don't know why, but I always invisioned Patrick Syewart to play Mr. Howell. They would probably get Eva Mendes to play Ginger. Rachel Bilson, from the OC to play Maryann. Rachel I think has the energy that Dawn had. Another person from the OC is Adam Brody. I wonder if he could pull off a Gilligan? I am stuck on the Professor and Skipper.

The toughest character to replace, I always believed would be Mrs. Howell. Natalie was a very unique actress. The easiest I believe would be Ginger. There are so many Gingers trying to break into the movies. I don't know if Helen Mirren would be too old to play Mrs. Howell. I believe she could pull it off well. I don't know why, but I always invisioned Patrick Syewart to play Mr. Howell. They would probably get Eva Mendes to play Ginger. Rachel Bilson, from the OC to play Maryann. Rachel I think has the energy that Dawn had. Another person from the OC is Adam Brody. I wonder if he could pull off a Gilligan? I am stuck on the Professor and Skipper.

Patrick Stewart would make a great Mr. Howell! And with Helen Mirren, a fellow Brit, you'd have two polished and very capable actors. Inspired choices, sir. :) I might have suggested Steve Martin, but he tends to go a bit overboard (no pun intended). I know Jim Backus was an ad-libbing ham, but there are ways of doing it so that it doesn't become annoying. Patrick Stweart would keep it subtle.

John Goodman as the Skipper? Or is he too old now?

The toughest character to replace, I always believed would be Mrs. Howell. Natalie was a very unique actress. The easiest I believe would be Ginger. There are so many Gingers trying to break into the movies. I don't know if Helen Mirren would be too old to play Mrs. Howell. I believe she could pull it off well. I don't know why, but I always invisioned Patrick Syewart to play Mr. Howell. They would probably get Eva Mendes to play Ginger. Rachel Bilson, from the OC to play Maryann. Rachel I think has the energy that Dawn had. Another person from the OC is Adam Brody. .

That's., besides me, another who votes for Bilson for Mary Ann!

I'm surprised to have never heard (here or anywhere else) Susan Sullivan suggested as a possible Lovey. I think Holland Taylor is a good choice and would prefer her over many others, but I would also argue that Sullivan would be better. For those that may not remember her, Susan Sullivan (like Holland Taylor and Natalie Schafer) is known for playing wealthy socialites. In this vain, you may remember her as Kitty Montgomery on the 90's sitcom Dharma and Greg or as Cameron Diaz's mother in My Best Friend's Wedding.

Sullivan's characters, particularly Kitty can be described as: mean, snobby, classy, and witty, with the ability to actually be a sweet person. Her portrayal of this particular character has always reminded me a lot of Lovey, for reasons that, given the aforementioned description, I don't think I need to explain to you. On top of that she has a comedic timing that to me, is reminiscent of Schafer's.

On the other hand, Taylor's characters are not as sweet. She's more of a straight man, er...woman. Her characters are mean and quick witted and that's the humor in her role. I'm not saying she's not talented, I respect her immensely. I'm just saying Sullivan is more Lovey-like to me, in that she evokes similarities of Natalie Schafer in ways Holland just doesn't. I will say this though, hopefully if you aren't following me, the comparison might make my point clearer. if they made a Gilmore Girls movie and Kelly Bishop was unavailable or didn't want to do it, I would think that Holland Taylor would make an excellent Emily Gilmore and that Susan Sullivan couldn't pull it off in a million years.

Sorry if I said too much btw.

Fun little topic. Well heres my "new" cast:

Gilligan: Jim Carrey
Skipper: John Goodman
Professor: Freddie Prinze Jr
Mary Ann: Alyson Hannigan
Ginger: Debra Messing
Mr. Howell: Robin Williams
Lovey:Kathleen Turner

Some may be a stretch haha but I kinda like that cast, seems like it could be fun. I obviously didnt go for all "look a likes" but I think these people would do a good job. I like alot of other answers too like Holland Taylor and Susan Sullivan, those are really good. Simon Baker too.

Mike O'Malley would be a good choice for "Skipper".

Fun little topic. Well heres my "new" cast:

Gilligan: Jim Carrey
Skipper: John Goodman
Professor: Freddie Prinze Jr
Mary Ann: Alyson Hannigan
Ginger: Debra Messing
Mr. Howell: Robin Williams
Lovey:Kathleen Turner

Some may be a stretch haha but I kinda like that cast, seems like it could be fun. I obviously didnt go for all "look a likes" but I think these people would do a good job. I like alot of other answers too like Holland Taylor and Susan Sullivan, those are really good. Simon Baker too.

Alyson Hannigan? Blech!