The first major deviations from what Gene Roddenberry wanted in TNG, that I can tell (besides casting Patrick Stewart as Picard), were: "Family", which he was against, but they did anyway; and "Redemption" because he didn't think Worf should be the focus of a major two-parter, but they did anyway.
Then it's taken to the next level with "The First Duty". I'm dead-certain Gene Roddenberry wouldn't have wanted Wesley dragged through the mud like that and made to become part of a cover-up. Ultimately Wesley comes forward but it was only due to pressure from Picard. He felt conflicted, and I don't think Gene would've wanted Wesley to feel conflicted at all.
Then comes not "I, Borg" where Picard is feeling bloody-minded and initially wanted Hugh to carry a virus to the Borg Collective, but what happens afterwards in "Descent, Part I" where Admiral Nacheyev tells Picard that the next time he has an opportunity to wipe out the Borg, he's to take it. I deeply suspect Gene wouldn't have wanted Starfleet to adopt this type of mentality, regardless of the circumstances.
The following year, comes the Maquis. Where there's visibly internal strife within the Federation and Starfleet. In "Journey's End", Wesley speaks out against Starfleet before joining The Traveller. I think Gene definitely wouldn't have liked the former part. Meanwhile, Picard has personal objections to having to relocate the inhabitants of Dorvan V because it reminds him of the forced relocation of Native Americans before. The first thing I think of is Andrew Jackson who was responsible for the Trail of Tears. Dorvan V's solution is to leave the Federation. So, the only way to not be forcibly relocated is to not be part of the "enlightened" Federation. I can't see Gene being too happy with this either.
Disclaimer: I like all of these episodes. I'm just looking at it from the point of view of Gene's Vision and what I think he would and wouldn't have approved of.
And if he didn't like the destruction of the Enterprise in TSFS, he wouldn't have liked the destruction of the Enterprise-D in Generations. That, to me, represents the icing on the cake, where the last remnants of Roddenberry's Star Trek were over.
So, no, I don't think Gene Roddenberry Star Trek continued on in spirit and lasted until 2005 like some say. I think his active involvement (even through delegation) ended in September 1989, when he had a stroke that confined him to a wheel chair. Rick Berman started doing things Gene Roddenberry wouldn't have done as early as the fourth season. -- As early as 1990! -- Then after the fifth season, they paid lip-service to Gene's Vision, but they were just going to do what they wanted to do, because now they were the ones having to make the creative decisions and had to do what they thought was best.
To break it down simply, this is how I see it in the TNG Era:
TNG Conception through first 18 episodes --> Gene Roddenberry is top dog, it's his show.
Late-Season 1 through beginning of Season 3 --> Gene Roddenberry delegates.
Season 3 through Mid-Season 5 --> Gene Roddenberry is a figurehead but doesn't really run things.
Mid-Season 5 through Generations --> Rick Berman has to decide where changes have to be made.
It's really Rick Berman Star Trek from 1989 to 2005.
EDITED TO ADD: Except for what I pointed out above, I think Gene Roddenberry largely would've approved of TNG all the way through "All Good Things". With the TNG Movies, DS9, VOY, or ENT, I lean towards probably not. The TNG Movies morphed TNG into a series of Action Flicks. We don't need to go into DS9 yet again. He was too misogynistic to approve of VOY (it sounds like he became worse about this, not better, as time went on). And I think he would've been against ENT because he'd be of the mindset of "That would take us in the wrong direction. Our mission is to go forward!," to quote Picard in "The Neutral Zone".
DOUBLE-EDIT: TNG is like The Ship of Theseus. "At what point is it really Rick Berman's Star Trek instead of Gene Roddenberry's?"